Diff of the two buildlogs: -- --- b1/build.log 2019-06-27 10:24:58.012839181 +0000 +++ b2/build.log 2019-06-27 11:13:24.236249749 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Jul 29 04:42:55 -12 2020 -I: pbuilder-time-stamp: 1596040975 +I: Current time: Fri Jun 28 00:25:06 +14 2019 +I: pbuilder-time-stamp: 1561631106 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -18,7 +18,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Tue Jun 18 22:58:34 2019 -12 +gpgv: Signature made Thu Jun 20 00:58:34 2019 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -37,6 +37,18 @@ dpkg-source: info: applying spelling.patch I: using fakeroot in build. I: Installing the build-deps +I: user script /srv/workspace/pbuilder/18873/tmp/hooks/D01_modify_environment starting +disorder-fs debug: Running on profitbricks-build12-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/18873/tmp/hooks/D01_modify_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -216,7 +228,7 @@ Get: 126 http://cdn-fastly.deb.debian.org/debian buster/main i386 libjpeg-dev all 1:1.5.2-2 [57.5 kB] Get: 127 http://cdn-fastly.deb.debian.org/debian buster/main i386 libhdf5-dev i386 1.10.4+repack-10 [2738 kB] Get: 128 http://cdn-fastly.deb.debian.org/debian buster/main i386 libjsoncpp-dev i386 1.7.4-3 [87.7 kB] -Fetched 83.8 MB in 15s (5416 kB/s) +Fetched 83.8 MB in 1min 14s (1135 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19231 files and directories currently installed.) @@ -756,9 +768,41 @@ Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). -0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 182 kB of additional disk space will be used. +Get:1 http://cdn-fastly.deb.debian.org/debian buster/main i386 libnumber-compare-perl all 0.03-1 [7642 B] +Get:2 http://cdn-fastly.deb.debian.org/debian buster/main i386 libtext-glob-perl all 0.10-1 [8362 B] +Get:3 http://cdn-fastly.deb.debian.org/debian buster/main i386 libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://cdn-fastly.deb.debian.org/debian buster/main i386 usrmerge all 21 [12.8 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 1s (92.1 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 39845 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.10-1_all.deb ... +Unpacking libtext-glob-perl (0.10-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_21_all.deb ... +Unpacking usrmerge (21) ... +Setting up libtext-glob-perl (0.10-1) ... +Setting up libnumber-compare-perl (0.03-1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (21) ... +The system has been successfully converted. +Processing triggers for man-db (2.8.5-2) ... +Not building database; man-db/auto-update is not 'true'. I: Building the package -I: Running cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package gatb-core dpkg-buildpackage: info: source version 1.4.1+git20181225.44d5a44+dfsg-3 dpkg-buildpackage: info: source distribution unstable @@ -847,7 +891,7 @@ debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg' dh_auto_build -a - cd obj-i686-linux-gnu && make -j18 "INSTALL=install --strip-program=true" + cd obj-i686-linux-gnu && make -j10 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core -B/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/CMakeFiles /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/CMakeFiles/progress.marks @@ -859,9 +903,9 @@ make[4]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/thirdparty /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/thirdparty/CMakeFiles/thirdparty_copy.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/CMakeFiles/gatbcore-dynamic.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/CMakeFiles/gatbcore-static.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/CMakeFiles/gatbcore-dynamic.dir/DependInfo.cmake --color= Scanning dependencies of target thirdparty_copy make[4]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' make -f thirdparty/CMakeFiles/thirdparty_copy.dir/build.make thirdparty/CMakeFiles/thirdparty_copy.dir/build @@ -872,54 +916,34 @@ cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/thirdparty && /usr/bin/cmake -E copy_if_different /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty/json/json.hpp /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/json/ make[4]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' [ 0%] Built target thirdparty_copy -Scanning dependencies of target gatbcore-dynamic -make[4]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' -make -f src/CMakeFiles/gatbcore-dynamic.dir/build.make src/CMakeFiles/gatbcore-dynamic.dir/build Scanning dependencies of target gatbcore-static make[4]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' make -f src/CMakeFiles/gatbcore-static.dir/build.make src/CMakeFiles/gatbcore-static.dir/build make[4]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' -make[4]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' -[ 0%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/Bank.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/Bank.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/Bank.cpp -[ 0%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankBinary.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankBinary.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp -[ 1%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankAlbum.cpp.o +[ 1%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankBinary.cpp.o [ 1%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankAlbum.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankAlbum.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankAlbum.cpp -[ 2%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/Bank.cpp.o -[ 2%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankHelpers.cpp.o -[ 3%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o -[ 3%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankFasta.cpp.o -[ 4%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankRandom.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/Bank.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/Bank.cpp -[ 4%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankFasta.cpp.o -[ 5%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankHelpers.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankBinary.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp +[ 1%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankFasta.cpp.o +[ 2%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankHelpers.cpp.o +[ 2%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankFasta.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankFasta.cpp -[ 5%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o 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/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankRandom.cpp -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankSplitter.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankSplitter.cpp -[ 7%] Building CXX object 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/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankHelpers.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankHelpers.cpp -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankRandom.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankRandom.cpp -[ 7%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankSplitter.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ 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/usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bcalm2/bcalm_algo.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankSplitter.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankSplitter.cpp -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp: In function 'bool gatb::core::bank::impl::checkMagic(FILE*)': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp:54:11: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread (&value, sizeof(value), 1, file); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/Bank.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/Bank.cpp +[ 4%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankSplitter.cpp.o +[ 4%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankRandom.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankSplitter.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankSplitter.cpp +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankRandom.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankRandom.cpp +Scanning dependencies of target gatbcore-dynamic +make[4]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' +make -f src/CMakeFiles/gatbcore-dynamic.dir/build.make src/CMakeFiles/gatbcore-dynamic.dir/build +make[4]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' +[ 4%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/Bank.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/Bank.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/Bank.cpp /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp: In function 'bool gatb::core::bank::impl::checkMagic(FILE*)': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp:54:11: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread (&value, sizeof(value), 1, file); @@ -928,15 +952,6 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp:453:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread (_bufferData->getBuffer(), sizeof( char),block_size, binary_read_file); // read a block of reads into the buffer ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp: In member function 'virtual void gatb::core::bank::impl::BankBinary::Iterator::next()': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp:453:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread (_bufferData->getBuffer(), sizeof( char),block_size, binary_read_file); // read a block of reads into the buffer - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, @@ -959,20 +974,10 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -[ 8%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/bcalm_algo.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/bcalm_algo.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp -[ 9%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bcalm2/logging.cpp.o +[ 4%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bcalm2/bglue_algo.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bcalm2/bglue_algo.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp +[ 5%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bcalm2/logging.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bcalm2/logging.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/logging.cpp -[ 9%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/bglue_algo.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/bglue_algo.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp -[ 9%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bcalm2/ograph.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bcalm2/ograph.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp -[ 9%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/logging.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/logging.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/logging.cpp -[ 10%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/BranchingAlgorithm.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/BranchingAlgorithm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp -[ 11%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/ograph.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/ograph.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/logging.cpp: In function 'long unsigned int gatb::core::debruijn::impl::logging(std::__cxx11::string)': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/logging.cpp:31:33: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'u_int64_t' {aka 'long long unsigned int'} [-Wformat=] snprintf (tmp, sizeof(tmp), " memory [current, maxRSS]: [%4lu, %4lu] MB ", @@ -980,44 +985,19 @@ mem, memMaxProcess); ~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/logging.cpp:31:33: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'u_int64_t' {aka 'long long unsigned int'} [-Wformat=] -[ 11%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Frontline.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Frontline.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Frontline.cpp -[ 11%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Graph.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Graph.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/logging.cpp: In function 'long unsigned int gatb::core::debruijn::impl::logging(std::__cxx11::string)': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/logging.cpp:31:33: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'u_int64_t' {aka 'long long unsigned int'} [-Wformat=] - snprintf (tmp, sizeof(tmp), " memory [current, maxRSS]: [%4lu, %4lu] MB ", - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - mem, memMaxProcess); - ~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/logging.cpp:31:33: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'u_int64_t' {aka 'long long unsigned int'} [-Wformat=] -[ 11%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/BranchingAlgorithm.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/BranchingAlgorithm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp -[ 12%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Frontline.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Frontline.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Frontline.cpp -[ 13%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/GraphUnitigs.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/GraphUnitigs.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp -[ 13%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/IterativeExtensions.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/IterativeExtensions.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.cpp -[ 14%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/LinkTigs.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/LinkTigs.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/LinkTigs.cpp +[ 5%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bcalm2/ograph.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bcalm2/ograph.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp +[ 6%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/BranchingAlgorithm.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/BranchingAlgorithm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -[ 14%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Graph.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Graph.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp -[ 14%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Simplifications.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Simplifications.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp -[ 14%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/GraphUnitigs.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/GraphUnitigs.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp -[ 15%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/IterativeExtensions.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/IterativeExtensions.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.cpp -[ 15%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Terminator.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Terminator.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.cpp -[ 16%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Traversal.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Traversal.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp +[ 6%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Frontline.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Frontline.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Frontline.cpp +[ 6%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Graph.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Graph.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, @@ -1028,6 +1008,8 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +[ 7%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/GraphUnitigs.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/GraphUnitigs.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, @@ -1039,6 +1021,8 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +[ 7%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/IterativeExtensions.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/IterativeExtensions.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, @@ -1048,36 +1032,19 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -[ 16%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] props->add (0, "host"); ^ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Frontline.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Frontline.cpp:24: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -[ 16%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/LinkTigs.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/LinkTigs.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/LinkTigs.cpp +[ 8%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/LinkTigs.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/LinkTigs.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/LinkTigs.cpp +[ 9%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankAlbum.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankAlbum.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankAlbum.cpp +[ 9%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Simplifications.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Simplifications.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp +[ 9%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Terminator.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Terminator.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, @@ -1088,6 +1055,8 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +[ 10%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Traversal.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Traversal.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:31: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] @@ -1103,99 +1072,8 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -[ 17%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Simplifications.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Simplifications.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp -[ 18%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/BloomAlgorithm.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/BloomAlgorithm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.hpp:27, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:20: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.cpp:24: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.cpp:20: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - props->add (0, "host"); - ^ -[ 18%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Terminator.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Terminator.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.cpp -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:31: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - props->add (0, "host"); - ^ -[ 18%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Traversal.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Traversal.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of 'bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >; Edge = gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >; Graph = gatb::core::debruijn::impl::GraphTemplate, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, boost::variant, gatb::core::debruijn::impl::GraphData<32>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<64>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<96>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<128>, boost::mpl::l_end> > > > > > >]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:852:16: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::set, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, std::less, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > >, std::allocator, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > > >::size_type' {aka 'unsigned int'} [-Wformat=] - if (debug) printf("%lu-bubble mean %d, stdev %.1f\n",consensuses.size(),mean,stdev); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 18%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/BloomBuilder.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/BloomBuilder.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomBuilder.cpp -[ 18%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/Configuration.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/Configuration.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Configuration.cpp -[ 19%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/ConfigurationAlgorithm.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/ConfigurationAlgorithm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/ConfigurationAlgorithm.cpp -[ 19%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/DebloomAlgorithm.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/DebloomAlgorithm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/DebloomAlgorithm.cpp -[ 20%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp +[ 10%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, @@ -1206,8 +1084,6 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -[ 20%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/BloomAlgorithm.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/BloomAlgorithm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, @@ -1218,25 +1094,6 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -[ 21%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/BloomBuilder.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/BloomBuilder.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomBuilder.cpp -[ 21%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/Configuration.cpp.o -[ 22%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/Configuration.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Configuration.cpp -[ 22%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/LinearCounter.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/LinearCounter.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/LinearCounter.cpp -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, @@ -1305,99 +1162,56 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of 'bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >; Edge = gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >; Graph = gatb::core::debruijn::impl::GraphTemplate, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, boost::variant, gatb::core::debruijn::impl::GraphData<32>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<64>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<96>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<128>, boost::mpl::l_end> > > > > > >]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:852:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::set, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, std::less, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > >, std::allocator, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > > >::size_type' {aka 'unsigned int'} [-Wformat=] if (debug) printf("%lu-bubble mean %d, stdev %.1f\n",consensuses.size(),mean,stdev); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 22%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/ConfigurationAlgorithm.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/ConfigurationAlgorithm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/ConfigurationAlgorithm.cpp -[ 22%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/MPHFAlgorithm.cpp.o +[ 11%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/BloomAlgorithm.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/BloomAlgorithm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp +[ 11%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/BloomBuilder.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/BloomBuilder.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomBuilder.cpp +[ 11%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/Configuration.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/Configuration.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Configuration.cpp +[ 12%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/ConfigurationAlgorithm.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/ConfigurationAlgorithm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/ConfigurationAlgorithm.cpp +[ 12%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/DebloomAlgorithm.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/DebloomAlgorithm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/DebloomAlgorithm.cpp +[ 12%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankBinary.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankBinary.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp +[ 13%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp: In function 'bool gatb::core::bank::impl::checkMagic(FILE*)': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp:54:11: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread (&value, sizeof(value), 1, file); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp: In member function 'virtual void gatb::core::bank::impl::BankBinary::Iterator::next()': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp:453:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread (_bufferData->getBuffer(), sizeof( char),block_size, binary_read_file); // read a block of reads into the buffer + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 13%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/LinearCounter.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/LinearCounter.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/LinearCounter.cpp +[ 13%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/MPHFAlgorithm.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/MPHFAlgorithm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<128>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] - memset (_data, 0, _blockSize*sizeof(Item)); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<128>::Count' declared here - struct Count : tools::misc::Abundance - ^~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<96>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] - memset (_data, 0, _blockSize*sizeof(Item)); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<96>::Count' declared here - struct Count : tools::misc::Abundance - ^~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<64>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] - memset (_data, 0, _blockSize*sizeof(Item)); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<64>::Count' declared here - struct Count : tools::misc::Abundance - ^~~~~ -[ 23%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/Model.cpp.o -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] - memset (_data, 0, _blockSize*sizeof(Item)); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<>::Count' declared here - struct Count : tools::misc::Abundance - ^~~~~ +[ 14%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/Model.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/Model.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp -[ 23%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/ModelData.cpp.o +[ 14%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/ModelData.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/ModelData.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/ModelData.cpp -[ 25%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/PartiInfo.cpp.o +[ 15%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/PartiInfo.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/PartiInfo.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp -[ 25%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/PartitionsCommand.cpp.o +[ 15%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/PartitionsCommand.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/PartitionsCommand.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp -[ 25%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/RepartitionAlgorithm.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial 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-I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/SortingCountAlgorithm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp -[ 26%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemCommon.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemCommon.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/FileSystemCommon.cpp -[ 27%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/DebloomAlgorithm.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/DebloomAlgorithm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/DebloomAlgorithm.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, @@ -1406,10 +1220,8 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -[ 28%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemLinux.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemLinux.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/FileSystemLinux.cpp -[ 28%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include 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-I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankConverterAlgorithm.cpp /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp: In member function 'void gatb::core::kmer::impl::Repartitor::printInfo()': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp:308:12: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'size_t' {aka 'unsigned int'} [-Wformat=] printf("Repartitor : nbMinimizers=%ld\n", nbMinimizers); @@ -1417,85 +1229,48 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp:309:61: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'u_int64_t' {aka 'long long unsigned int'} [-Wformat=] for (u_int64_t ii=0; ii::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -[ 36%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Algorithm.cpp.o +[ 23%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Algorithm.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ 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-Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/SortingCountAlgorithm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp -[ 37%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Histogram.cpp.o +[ 25%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Histogram.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Histogram.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Histogram.cpp -[ 37%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/OptionsParser.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/OptionsParser.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/OptionsParser.cpp -[ 38%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemCommon.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemCommon.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/FileSystemCommon.cpp -[ 38%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemLinux.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemLinux.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/FileSystemLinux.cpp -[ 38%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Progress.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Progress.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp -[ 39%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Property.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Property.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp -[ 40%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemMacos.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemMacos.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/FileSystemMacos.cpp -[ 40%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/System.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/System.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/System.cpp -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp: In member function 'void gatb::core::kmer::impl::Repartitor::printInfo()': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp:308:12: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'size_t' {aka 'unsigned int'} [-Wformat=] - printf("Repartitor : nbMinimizers=%ld\n", nbMinimizers); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp:309:61: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'u_int64_t' {aka 'long long unsigned int'} [-Wformat=] - for (u_int64_t ii=0; ii::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -[ 40%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/SystemInfoCommon.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/SystemInfoCommon.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/SystemInfoCommon.cpp +[ 25%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/OptionsParser.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/OptionsParser.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/OptionsParser.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, @@ -1520,6 +1295,8 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +[ 25%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankFasta.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankFasta.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankFasta.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, @@ -1531,12 +1308,8 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp: In member function 'virtual void gatb::core::tools::misc::impl::Properties::setInt(const string&, const int64_t&)': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp:438:39: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] - snprintf (buffer, sizeof(buffer), "%ld", value); - ^~~~~ ~~~~~ -[ 41%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/ThreadLinux.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/ThreadLinux.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/ThreadLinux.cpp +[ 25%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Progress.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Progress.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp: In member function 'void Leon::createBloom()': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:323:47: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] getInfo()->add (0, "Abundance threshold"); @@ -1576,21 +1349,6 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:1429:38: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] getInfo()->add(0, "Decompression"); ^ -[ 41%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/ThreadMacos.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/ThreadMacos.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/ThreadMacos.cpp -[ 42%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/collections/impl/Bloom.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/collections/impl/Bloom.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/Bloom.cpp -[ 42%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/DnaCoder.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/DnaCoder.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.cpp -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp: In member function 'virtual void gatb::core::tools::misc::impl::ProgressTimerAndSystem::fillBuffer(double)': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp:350:33: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'u_int64_t' {aka 'long long unsigned int'} [-Wformat=] - snprintf (tmp, sizeof(tmp), " cpu: %5.1f %% mem: [%4lu, %4lu, %4lu] MB ", - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp:352:9: - mem, _memMax, memMaxProcess - ~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp:350:33: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'u_int64_t' {aka 'long long unsigned int'} [-Wformat=] -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp:350:33: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'u_int64_t' {aka 'long long unsigned int'} [-Wformat=] In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, @@ -1610,12 +1368,8 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: 'class gatb::core::tools::math::NativeInt8' declared here class NativeInt8 : private misc::ArrayData ^~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/ThreadLinux.cpp: In constructor 'gatb::core::system::impl::ThreadLinux::ThreadLinux(void* (*)(void*), void*)': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/ThreadLinux.cpp:51:7: warning: variable 'ret' set but not used [-Wunused-but-set-variable] - int ret = pthread_attr_init ( &tattr ) ; - ^~~ -[ 42%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/HeaderCoder.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/HeaderCoder.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp +[ 26%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Property.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Property.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, @@ -1635,8 +1389,6 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: 'class gatb::core::tools::math::NativeInt8' declared here class NativeInt8 : private misc::ArrayData ^~~~~~~~~~ -[ 43%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/Leon.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/Leon.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, @@ -1694,148 +1446,10 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: 'class gatb::core::tools::math::NativeInt64' declared here class NativeInt64 ^~~~~~~~~~~ -[ 43%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/TimeInfo.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/TimeInfo.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/TimeInfo.cpp -[ 43%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/RangeCoder.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/designpattern/impl/Observer.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Observer.cpp -[ 45%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Tokenizer.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat 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-D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Tool.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Tool.cpp -[ 45%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/api/Data.cpp.o -[ 45%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/XmlReader.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 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-D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/XmlReader.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/XmlReader.cpp -[ 46%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Algorithm.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Algorithm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.cpp -[ 46%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Histogram.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Histogram.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Histogram.cpp -[ 47%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/storage/impl/Storage.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/storage/impl/Storage.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.cpp -[ 48%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/OptionsParser.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/OptionsParser.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/OptionsParser.cpp -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.cpp:21: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.hpp:35, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:21: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -[ 48%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Progress.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Progress.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp -[ 48%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/storage/impl/StorageTools.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/storage/impl/StorageTools.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageTools.cpp -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -[ 50%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_128.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp -[ 50%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_32.cpp.o -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp: In member function 'void Leon::createBloom()': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:323:47: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - getInfo()->add (0, "Abundance threshold"); - ^ -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:328:49: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - getInfo()->add (0, "Abundance threshold"); - ^ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp: In member function 'void Leon::executeCompression()': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:404:43: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - getInfo()->add (0, "Input format: FastQ"); - ^ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:410:66: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - getInfo()->add (0, "Quality compression: LOSSLESS mode"); - ^ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:412:106: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - getInfo()->add (0, "Quality compression: lossy mode (use '-lossless' for lossless compression)"); - ^ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:422:43: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - getInfo()->add (0, "Input format: FastA"); - ^ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:429:123: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - getInfo()->add (0, "Input format: unknown. Input extension must be one among fasta (.fa, .fasta) or fastq (.fq, .fastq)"); - ^ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp: In member function 'void Leon::endCompression()': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:727:40: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - getInfo()->add(0, "End compression"); - ^ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp: In member function 'void Leon::endHeaderCompression()': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:883:44: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - getInfo()->add(0, "End Header compression"); - ^ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp: In member function 'void Leon::endDnaCompression()': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:970:47: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - getInfo()->add(0, "End Sequence compression"); - ^ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp: In member function 'void Leon::executeDecompression()': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:1429:38: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - getInfo()->add(0, "Decompression"); - ^ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.cpp:21: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt8; size_t = unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt8]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class gatb::core::tools::math::NativeInt8'; use assignment or value-initialization instead [-Wclass-memaccess] - memset (_data, 0, _blockSize*sizeof(Item)); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.cpp:21: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: 'class gatb::core::tools::math::NativeInt8' declared here - class NativeInt8 : private misc::ArrayData - ^~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.hpp:35, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:21: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt8; size_t = unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt8]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class gatb::core::tools::math::NativeInt8'; use assignment or value-initialization instead [-Wclass-memaccess] - memset (_data, 0, _blockSize*sizeof(Item)); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.hpp:35, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:21: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: 'class gatb::core::tools::math::NativeInt8' declared here - class NativeInt8 : private misc::ArrayData - ^~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp: In member function 'virtual void gatb::core::tools::misc::impl::Properties::setInt(const string&, const int64_t&)': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp:438:39: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] + snprintf (buffer, sizeof(buffer), "%ld", value); + ^~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp: In member function 'virtual void gatb::core::tools::misc::impl::ProgressTimerAndSystem::fillBuffer(double)': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp:350:33: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'u_int64_t' {aka 'long long unsigned int'} [-Wformat=] snprintf (tmp, sizeof(tmp), " cpu: %5.1f %% mem: [%4lu, %4lu, %4lu] MB ", @@ -1845,63 +1459,18 @@ ~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp:350:33: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'u_int64_t' {aka 'long long unsigned int'} [-Wformat=] /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp:350:33: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'u_int64_t' {aka 'long long unsigned int'} [-Wformat=] -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] - memset (_data, 0, _blockSize*sizeof(Item)); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:71, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<>::Count' declared here - struct Count : tools::misc::Abundance - ^~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt8; size_t = unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt8]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class gatb::core::tools::math::NativeInt8'; use assignment or value-initialization instead [-Wclass-memaccess] - memset (_data, 0, _blockSize*sizeof(Item)); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: 'class gatb::core::tools::math::NativeInt8' declared here - class NativeInt8 : private misc::ArrayData - ^~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt64; size_t = unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt64]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class gatb::core::tools::math::NativeInt64'; use assignment or value-initialization instead [-Wclass-memaccess] - memset (_data, 0, _blockSize*sizeof(Item)); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: 'class gatb::core::tools::math::NativeInt64' declared here - class NativeInt64 - ^~~~~~~~~~~ +[ 26%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/TimeInfo.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/TimeInfo.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/TimeInfo.cpp +[ 27%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Tokenizer.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Tokenizer.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Tokenizer.cpp +[ 27%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Tool.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o 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CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/XmlReader.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/XmlReader.cpp +[ 27%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankHelpers.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankHelpers.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankHelpers.cpp +[ 28%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/storage/impl/Storage.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/storage/impl/Storage.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, @@ -1917,8 +1486,12 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: 'class gatb::core::tools::math::NativeInt8' declared here class NativeInt8 : private misc::ArrayData ^~~~~~~~~~ -[ 50%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Property.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Property.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp +[ 28%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/storage/impl/StorageTools.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/storage/impl/StorageTools.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageTools.cpp +[ 29%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_128.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp +[ 30%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankRandom.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankRandom.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankRandom.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with unsigned int span = 128]': @@ -1929,20 +1502,14 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ -[ 51%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/TimeInfo.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial 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51%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Tokenizer.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Tokenizer.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Tokenizer.cpp -[ 52%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_96.cpp.o +[ 31%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_96.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_96.cpp -[ 52%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_128.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function 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-I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankSplitter.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankSplitter.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with unsigned int span = 32]': @@ -1953,12 +1520,6 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ -[ 53%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Tool.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include 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-I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with unsigned int span = 64]': @@ -1979,24 +1540,24 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ +[ 31%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_128.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -[ 54%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/storage/impl/Storage.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 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-ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_64.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp -[ 55%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/storage/impl/StorageTools.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/storage/impl/StorageTools.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageTools.cpp +[ 32%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_32.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:3: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In instantiation of 'void gatb::core::debruijn::impl::graph3::debruijn() [with unsigned int span = 128]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:31:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:236:10: warning: unused variable 'debug_index' [-Wunused-variable] uint debug_index = 0; ^~~~~~~~~~~ +[ 33%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/bcalm_algo.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/bcalm_algo.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of 'uint64_t boomphf::mphf::totalBitSize() [with elem_t = long long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long long unsigned int]': @@ -2013,16 +1574,6 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:258:18: warning: unused variable 'first_index' [-Wunused-variable] uint32_t first_index = markedSequence_index; ^~~~~~~~~~~ -[ 55%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_128.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:2: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -[ 56%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_32.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, @@ -2041,23 +1592,12 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<128>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.cpp:22: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt8; size_t = unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt8]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class gatb::core::tools::math::NativeInt8'; use assignment or value-initialization instead [-Wclass-memaccess] - memset (_data, 0, _blockSize*sizeof(Item)); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.cpp:22: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: 'class gatb::core::tools::math::NativeInt8' declared here - class NativeInt8 : private misc::ArrayData - ^~~~~~~~~~ -[ 56%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_64.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_64.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:2: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:3: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In instantiation of 'void gatb::core::debruijn::impl::graph3::debruijn() [with unsigned int span = 32]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:31:16: required from here @@ -2080,34 +1620,45 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:258:18: warning: unused variable 'first_index' [-Wunused-variable] uint32_t first_index = markedSequence_index; ^~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:1: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<32>::Count; size_t = unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<32>::Count]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<32>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] + memset (_data, 0, _blockSize*sizeof(Item)); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.h:15, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:1: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<32>::Count' declared here + struct Count : tools::misc::Abundance + ^~~~~ +[ 33%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/bglue_algo.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/bglue_algo.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp +[ 33%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_64.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_64.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -[ 56%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_96.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_96.cpp -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with unsigned int span = 128]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp:13:17: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] - while(uid<4 && skid < superKmerLen) - ~~~~~^~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] - if(skid >= superKmerLen) break; - ~~~~~^~~~~~~~~~~~~~~ -[ 57%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_128.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:3: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In instantiation of 'void gatb::core::debruijn::impl::graph3::debruijn() [with unsigned int span = 64]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:31:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:236:10: warning: unused variable 'debug_index' [-Wunused-variable] uint debug_index = 0; ^~~~~~~~~~~ -[ 57%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_96.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of 'uint64_t boomphf::mphf::totalBitSize() [with elem_t = long long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long long unsigned int]': @@ -2117,6 +1668,8 @@ printf("final hash %12lu bits (%.2f %%) (nb in final hash %lu)\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::unordered_map, std::equal_to, std::allocator > >::size_type' {aka 'unsigned int'} [-Wformat=] +[ 33%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_96.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp: In instantiation of 'void gatb::core::debruijn::impl::determine_order_sequences(std::vector >&, const std::vector >&, int, bool) [with int SPAN = 64]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:1106:48: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with unsigned int SPAN = 64; std::__cxx11::string = std::__cxx11::basic_string]' @@ -2129,48 +1682,6 @@ from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:1: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<32>::Count; size_t = unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<32>::Count]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<32>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] - memset (_data, 0, _blockSize*sizeof(Item)); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.h:15, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:1: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<32>::Count' declared here - struct Count : tools::misc::Abundance - ^~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with unsigned int span = 32]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp:13:17: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] - while(uid<4 && skid < superKmerLen) - ~~~~~^~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] - if(skid >= superKmerLen) break; - ~~~~~^~~~~~~~~~~~~~~ -[ 58%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_128.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with unsigned int span = 64]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp:13:17: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] - while(uid<4 && skid < superKmerLen) - ~~~~~^~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] - if(skid >= superKmerLen) break; - ~~~~~^~~~~~~~~~~~~~~ -[ 58%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_32.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = unsigned int]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]' @@ -2184,28 +1695,47 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<64>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_96.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with unsigned int span = 96]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_96.cpp:13:17: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] - while(uid<4 && skid < superKmerLen) - ~~~~~^~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] - if(skid >= superKmerLen) break; - ~~~~~^~~~~~~~~~~~~~~ +[ 34%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_128.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp +[ 34%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_32.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:2: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +[ 34%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/logging.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/logging.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/logging.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:3: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In instantiation of 'void gatb::core::debruijn::impl::graph3::debruijn() [with unsigned int span = 96]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:31:16: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:236:10: warning: unused variable 'debug_index' [-Wunused-variable] + uint debug_index = 0; + ^~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/logging.cpp: In function 'long unsigned int gatb::core::debruijn::impl::logging(std::__cxx11::string)': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/logging.cpp:31:33: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'u_int64_t' {aka 'long long unsigned int'} [-Wformat=] + snprintf (tmp, sizeof(tmp), " memory [current, maxRSS]: [%4lu, %4lu] MB ", + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + mem, memMaxProcess); + ~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/logging.cpp:31:33: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'u_int64_t' {aka 'long long unsigned int'} [-Wformat=] In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of 'uint64_t boomphf::mphf::totalBitSize() [with elem_t = long long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long long unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:765:60: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with unsigned int SPAN = 96; std::__cxx11::string = std::__cxx11::basic_string]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:29:9: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::unordered_map, std::equal_to, std::allocator > >::size_type' {aka 'unsigned int'} [-Wformat=] + printf("final hash %12lu bits (%.2f %%) (nb in final hash %lu)\n", + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::unordered_map, std::equal_to, std::allocator > >::size_type' {aka 'unsigned int'} [-Wformat=] +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp: In instantiation of 'void gatb::core::debruijn::impl::determine_order_sequences(std::vector >&, const std::vector >&, int, bool) [with int SPAN = 96]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:1106:48: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with unsigned int SPAN = 96; std::__cxx11::string = std::__cxx11::basic_string]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:29:9: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:258:18: warning: unused variable 'first_index' [-Wunused-variable] + uint32_t first_index = markedSequence_index; + ^~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:6: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 128]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:14:16: required from here @@ -2221,12 +1751,6 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:3: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In instantiation of 'void gatb::core::debruijn::impl::graph3::debruijn() [with unsigned int span = 128]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:31:16: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:236:10: warning: unused variable 'debug_index' [-Wunused-variable] - uint debug_index = 0; - ^~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with unsigned int span = 128]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 128]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:14:16: required from here @@ -2245,32 +1769,41 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ -[ 59%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_64.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_64.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:2: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of 'uint64_t boomphf::mphf::totalBitSize() [with elem_t = long long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long long unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:765:60: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with unsigned int SPAN = 128; std::__cxx11::string = std::__cxx11::basic_string]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:29:9: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::unordered_map, std::equal_to, std::allocator > >::size_type' {aka 'unsigned int'} [-Wformat=] - printf("final hash %12lu bits (%.2f %%) (nb in final hash %lu)\n", - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::unordered_map, std::equal_to, std::allocator > >::size_type' {aka 'unsigned int'} [-Wformat=] -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:2: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp: In instantiation of 'void gatb::core::debruijn::impl::determine_order_sequences(std::vector >&, const std::vector >&, int, bool) [with int SPAN = 128]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:1106:48: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with unsigned int SPAN = 128; std::__cxx11::string = std::__cxx11::basic_string]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:29:9: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:258:18: warning: unused variable 'first_index' [-Wunused-variable] - uint32_t first_index = markedSequence_index; - ^~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:3: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In instantiation of 'void gatb::core::debruijn::impl::graph3::debruijn() [with unsigned int span = 96]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:31:16: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:236:10: warning: unused variable 'debug_index' [-Wunused-variable] - uint debug_index = 0; - ^~~~~~~~~~~ -[ 59%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_96.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:6: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 32]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:14:16: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountFileNames.size(); ii++) + ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountFileNames.size(); ii++) + ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 35%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/ograph.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/ograph.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with unsigned int span = 32]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 32]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:14:16: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] + while(filenames.size() > _reduceTarget) + ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< currentFiles.size(); ii++) + ~~^~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< currentFiles.size(); ii++) + ~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: @@ -2321,30 +1854,6 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:195:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] result.add (0, "histogram"); ~~~~~~~~~~~^~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of 'uint64_t boomphf::mphf::totalBitSize() [with elem_t = long long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long long unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:765:60: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with unsigned int SPAN = 96; std::__cxx11::string = std::__cxx11::basic_string]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:29:9: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::unordered_map, std::equal_to, std::allocator > >::size_type' {aka 'unsigned int'} [-Wformat=] - printf("final hash %12lu bits (%.2f %%) (nb in final hash %lu)\n", - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::unordered_map, std::equal_to, std::allocator > >::size_type' {aka 'unsigned int'} [-Wformat=] -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:6: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 32]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:14:16: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountFileNames.size(); ii++) - ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountFileNames.size(); ii++) - ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, @@ -2358,75 +1867,6 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp: In instantiation of 'void gatb::core::debruijn::impl::determine_order_sequences(std::vector >&, const std::vector >&, int, bool) [with int SPAN = 96]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:1106:48: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with unsigned int SPAN = 96; std::__cxx11::string = std::__cxx11::basic_string]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:29:9: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:258:18: warning: unused variable 'first_index' [-Wunused-variable] - uint32_t first_index = markedSequence_index; - ^~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with unsigned int span = 32]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 32]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:14:16: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] - while(filenames.size() > _reduceTarget) - ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< currentFiles.size(); ii++) - ~~^~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< currentFiles.size(); ii++) - ~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<128>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] - memset (_data, 0, _blockSize*sizeof(Item)); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<128>::Count' declared here - struct Count : tools::misc::Abundance - ^~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt64; size_t = unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt64]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class gatb::core::tools::math::NativeInt64'; use assignment or value-initialization instead [-Wclass-memaccess] - memset (_data, 0, _blockSize*sizeof(Item)); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/Integer.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: 'class gatb::core::tools::math::NativeInt64' declared here - class NativeInt64 - ^~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: @@ -2444,6 +1884,24 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 32; Derived = gatb::core::kmer::impl::CountProcessorSolidityOne<32>]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:1: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<96>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] + memset (_data, 0, _blockSize*sizeof(Item)); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.h:15, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:1: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<96>::Count' declared here + struct Count : tools::misc::Abundance + ^~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 32; Derived = gatb::core::kmer::impl::CountProcessorSolidityMax<32>]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] @@ -2493,18 +1951,21 @@ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:1: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = unsigned int]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<128>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.h:15, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:1: +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<128>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ @@ -2515,6 +1976,29 @@ from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt64; size_t = unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt64]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class gatb::core::tools::math::NativeInt64'; use assignment or value-initialization instead [-Wclass-memaccess] + memset (_data, 0, _blockSize*sizeof(Item)); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/Integer.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: 'class gatb::core::tools::math::NativeInt64' declared here + class NativeInt64 + ^~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = unsigned int]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]' @@ -2552,24 +2036,10 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: 'class gatb::core::tools::math::NativeInt64' declared here class NativeInt64 ^~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:1: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<96>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] - memset (_data, 0, _blockSize*sizeof(Item)); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.h:15, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:1: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<96>::Count' declared here - struct Count : tools::misc::Abundance - ^~~~~ +[ 36%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_64.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_64.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp +[ 36%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/BranchingAlgorithm.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/BranchingAlgorithm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:6: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 64]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:14:16: required from here @@ -2603,23 +2073,6 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ -[ 59%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_32.cpp.o -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:6: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 96]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:14:16: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountFileNames.size(); ii++) - ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountFileNames.size(); ii++) - ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: @@ -2643,24 +2096,6 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 64; Derived = gatb::core::kmer::impl::CountProcessorSolidityMin<64>]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with unsigned int span = 96]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 96]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:14:16: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] - while(filenames.size() > _reduceTarget) - ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< currentFiles.size(); ii++) - ~~^~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< currentFiles.size(); ii++) - ~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:28, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: @@ -2688,6 +2123,16 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:195:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] result.add (0, "histogram"); ~~~~~~~~~~~^~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, @@ -2745,6 +2190,70 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: 'class gatb::core::tools::math::NativeInt64' declared here class NativeInt64 ^~~~~~~~~~~ +[ 37%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Frontline.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Frontline.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Frontline.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Frontline.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Frontline.cpp:24: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +[ 37%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_96.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp +[ 37%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Graph.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Graph.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:6: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 96]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:14:16: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountFileNames.size(); ii++) + ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountFileNames.size(); ii++) + ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with unsigned int span = 96]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 96]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:14:16: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] + while(filenames.size() > _reduceTarget) + ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< currentFiles.size(); ii++) + ~~^~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< currentFiles.size(); ii++) + ~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + props->add (0, "host"); + ^ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: @@ -2852,245 +2361,20 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: 'class gatb::core::tools::math::NativeInt64' declared here class NativeInt64 ^~~~~~~~~~~ -[ 60%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_64.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_64.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp -[ 60%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_96.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp -[ 60%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_128.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:2: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:3: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In instantiation of 'void gatb::core::debruijn::impl::graph3::debruijn() [with unsigned int span = 32]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:31:16: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:236:10: warning: unused variable 'debug_index' [-Wunused-variable] - uint debug_index = 0; - ^~~~~~~~~~~ -[ 61%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_32.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:2: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of 'uint64_t boomphf::mphf::totalBitSize() [with elem_t = long long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long long unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:765:60: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with unsigned int SPAN = 32; std::__cxx11::string = std::__cxx11::basic_string]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:29:9: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::unordered_map, std::equal_to, std::allocator > >::size_type' {aka 'unsigned int'} [-Wformat=] - printf("final hash %12lu bits (%.2f %%) (nb in final hash %lu)\n", - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::unordered_map, std::equal_to, std::allocator > >::size_type' {aka 'unsigned int'} [-Wformat=] -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:2: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp: In instantiation of 'void gatb::core::debruijn::impl::determine_order_sequences(std::vector >&, const std::vector >&, int, bool) [with int SPAN = 32]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:1106:48: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with unsigned int SPAN = 32; std::__cxx11::string = std::__cxx11::basic_string]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:29:9: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:258:18: warning: unused variable 'first_index' [-Wunused-variable] - uint32_t first_index = markedSequence_index; - ^~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:2: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:3: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In instantiation of 'void gatb::core::debruijn::impl::graph3::debruijn() [with unsigned int span = 64]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:31:16: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:236:10: warning: unused variable 'debug_index' [-Wunused-variable] - uint debug_index = 0; - ^~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:2: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of 'uint64_t boomphf::mphf::totalBitSize() [with elem_t = long long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long long unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:765:60: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with unsigned int SPAN = 64; std::__cxx11::string = std::__cxx11::basic_string]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:29:9: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::unordered_map, std::equal_to, std::allocator > >::size_type' {aka 'unsigned int'} [-Wformat=] - printf("final hash %12lu bits (%.2f %%) (nb in final hash %lu)\n", - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::unordered_map, std::equal_to, std::allocator > >::size_type' {aka 'unsigned int'} [-Wformat=] -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:1: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<32>::Count; size_t = unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<32>::Count]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<32>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] - memset (_data, 0, _blockSize*sizeof(Item)); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.h:15, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:1: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<32>::Count' declared here - struct Count : tools::misc::Abundance - ^~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:6: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 128]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:14:16: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountFileNames.size(); ii++) - ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:2: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp: In instantiation of 'void gatb::core::debruijn::impl::determine_order_sequences(std::vector >&, const std::vector >&, int, bool) [with int SPAN = 64]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:1106:48: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with unsigned int SPAN = 64; std::__cxx11::string = std::__cxx11::basic_string]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:29:9: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:258:18: warning: unused variable 'first_index' [-Wunused-variable] - uint32_t first_index = markedSequence_index; - ^~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountFileNames.size(); ii++) - ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with unsigned int span = 128]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 128]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:14:16: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] - while(filenames.size() > _reduceTarget) - ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< currentFiles.size(); ii++) - ~~^~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< currentFiles.size(); ii++) - ~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:3: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In instantiation of 'void gatb::core::debruijn::impl::graph3::debruijn() [with unsigned int span = 96]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:31:16: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:236:10: warning: unused variable 'debug_index' [-Wunused-variable] - uint debug_index = 0; - ^~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of 'uint64_t boomphf::mphf::totalBitSize() [with elem_t = long long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long long unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:765:60: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with unsigned int SPAN = 96; std::__cxx11::string = std::__cxx11::basic_string]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:29:9: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::unordered_map, std::equal_to, std::allocator > >::size_type' {aka 'unsigned int'} [-Wformat=] - printf("final hash %12lu bits (%.2f %%) (nb in final hash %lu)\n", - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::unordered_map, std::equal_to, std::allocator > >::size_type' {aka 'unsigned int'} [-Wformat=] -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 128; Derived = gatb::core::kmer::impl::CountProcessorSoliditySum<128>]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - result.add (0, "kmers"); - ~~~~~~~~~~~^~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 128; Derived = gatb::core::kmer::impl::CountProcessorSolidityAll<128>]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 128; Derived = gatb::core::kmer::impl::CountProcessorSolidityCustom<128>]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 128; Derived = gatb::core::kmer::impl::CountProcessorSolidityOne<128>]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 128; Derived = gatb::core::kmer::impl::CountProcessorSolidityMax<128>]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 128; Derived = gatb::core::kmer::impl::CountProcessorSolidityMin<128>]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp: In instantiation of 'void gatb::core::debruijn::impl::determine_order_sequences(std::vector >&, const std::vector >&, int, bool) [with int SPAN = 96]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:1106:48: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with unsigned int SPAN = 96; std::__cxx11::string = std::__cxx11::basic_string]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:29:9: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:258:18: warning: unused variable 'first_index' [-Wunused-variable] - uint32_t first_index = markedSequence_index; - ^~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:28, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorDump::getProperties() const [with unsigned int span = 128]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:159:35: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:172:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - result.add (0, "partitions"); - ~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:27, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of 'void gatb::core::kmer::impl::CountProcessorHistogram::end() [with unsigned int span = 128]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:104:10: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:117:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii<= _histogram->getLength(); ii++) - ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:120:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] - for(int jj=0; jj<= _histogram->getLength2(); jj++) - ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:135:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=1; ii<= _histogram->getLength(); ii++) - ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorHistogram::getProperties() const [with unsigned int span = 128]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:191:35: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:195:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - result.add (0, "histogram"); - ~~~~~~~~~~~^~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with unsigned int span = 128]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1057:5: required from 'void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with unsigned int span = 128; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<128>::SuperKmer]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1048:8: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] - while(uid<4 && skid < superKmerLen) - ~~~~~^~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] - if(skid >= superKmerLen) break; - ~~~~~^~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:6: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 32]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:14:16: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountFileNames.size(); ii++) - ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountFileNames.size(); ii++) - ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = unsigned int]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<128>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<128>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ @@ -3098,188 +2382,57 @@ from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt64; size_t = unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt64]' + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class gatb::core::tools::math::NativeInt64'; use assignment or value-initialization instead [-Wclass-memaccess] +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<96>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/Integer.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: 'class gatb::core::tools::math::NativeInt64' declared here - class NativeInt64 - ^~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with unsigned int span = 32]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 32]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:14:16: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] - while(filenames.size() > _reduceTarget) - ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< currentFiles.size(); ii++) - ~~^~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< currentFiles.size(); ii++) - ~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<96>::Count' declared here + struct Count : tools::misc::Abundance + ^~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:1: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = unsigned int]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<64>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.h:15, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:1: +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<64>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 32; Derived = gatb::core::kmer::impl::CountProcessorSoliditySum<32>]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - result.add (0, "kmers"); - ~~~~~~~~~~~^~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 32; Derived = gatb::core::kmer::impl::CountProcessorSolidityAll<32>]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 32; Derived = gatb::core::kmer::impl::CountProcessorSolidityCustom<32>]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 32; Derived = gatb::core::kmer::impl::CountProcessorSolidityOne<32>]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 32; Derived = gatb::core::kmer::impl::CountProcessorSolidityMax<32>]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 32; Derived = gatb::core::kmer::impl::CountProcessorSolidityMin<32>]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:28, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorDump::getProperties() const [with unsigned int span = 32]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:159:35: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:172:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - result.add (0, "partitions"); - ~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:27, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of 'void gatb::core::kmer::impl::CountProcessorHistogram::end() [with unsigned int span = 32]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:104:10: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:117:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii<= _histogram->getLength(); ii++) - ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:120:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] - for(int jj=0; jj<= _histogram->getLength2(); jj++) - ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:135:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=1; ii<= _histogram->getLength(); ii++) - ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorHistogram::getProperties() const [with unsigned int span = 32]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:191:35: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:195:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - result.add (0, "histogram"); - ~~~~~~~~~~~^~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with unsigned int span = 32]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1057:5: required from 'void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with unsigned int span = 32; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<>::SuperKmer]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1048:8: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] - while(uid<4 && skid < superKmerLen) - ~~~~~^~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] - if(skid >= superKmerLen) break; - ~~~~~^~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:1: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<96>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] - memset (_data, 0, _blockSize*sizeof(Item)); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.h:15, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:1: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<96>::Count' declared here - struct Count : tools::misc::Abundance - ^~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = unsigned int]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt64; size_t = unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt64]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class gatb::core::tools::math::NativeInt64'; use assignment or value-initialization instead [-Wclass-memaccess] - memset (_data, 0, _blockSize*sizeof(Item)); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/Integer.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: 'class gatb::core::tools::math::NativeInt64' declared here - class NativeInt64 - ^~~~~~~~~~~ -[ 61%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_128.cpp.o +[ 37%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_128.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_128.cpp +[ 38%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_32.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_32.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, @@ -3301,156 +2454,8 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: 'class gatb::core::tools::math::NativeInt8' declared here class NativeInt8 : private misc::ArrayData ^~~~~~~~~~ -[ 61%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_64.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_64.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:6: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 64]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:14:16: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountFileNames.size(); ii++) - ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountFileNames.size(); ii++) - ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with unsigned int span = 64]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 64]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:14:16: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] - while(filenames.size() > _reduceTarget) - ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< currentFiles.size(); ii++) - ~~^~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< currentFiles.size(); ii++) - ~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 64; Derived = gatb::core::kmer::impl::CountProcessorSoliditySum<64>]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - result.add (0, "kmers"); - ~~~~~~~~~~~^~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 64; Derived = gatb::core::kmer::impl::CountProcessorSolidityAll<64>]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 64; Derived = gatb::core::kmer::impl::CountProcessorSolidityCustom<64>]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 64; Derived = gatb::core::kmer::impl::CountProcessorSolidityOne<64>]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 64; Derived = gatb::core::kmer::impl::CountProcessorSolidityMax<64>]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 64; Derived = gatb::core::kmer::impl::CountProcessorSolidityMin<64>]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:28, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorDump::getProperties() const [with unsigned int span = 64]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:159:35: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:172:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - result.add (0, "partitions"); - ~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:27, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of 'void gatb::core::kmer::impl::CountProcessorHistogram::end() [with unsigned int span = 64]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:104:10: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:117:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii<= _histogram->getLength(); ii++) - ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:120:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] - for(int jj=0; jj<= _histogram->getLength2(); jj++) - ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:135:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=1; ii<= _histogram->getLength(); ii++) - ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorHistogram::getProperties() const [with unsigned int span = 64]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:191:35: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:195:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - result.add (0, "histogram"); - ~~~~~~~~~~~^~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with unsigned int span = 64]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1057:5: required from 'void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with unsigned int span = 64; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<64>::SuperKmer]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1048:8: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] - while(uid<4 && skid < superKmerLen) - ~~~~~^~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] - if(skid >= superKmerLen) break; - ~~~~~^~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<64>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] - memset (_data, 0, _blockSize*sizeof(Item)); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<64>::Count' declared here - struct Count : tools::misc::Abundance - ^~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt64; size_t = unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt64]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class gatb::core::tools::math::NativeInt64'; use assignment or value-initialization instead [-Wclass-memaccess] - memset (_data, 0, _blockSize*sizeof(Item)); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/Integer.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: 'class gatb::core::tools::math::NativeInt64' declared here - class NativeInt64 - ^~~~~~~~~~~ -[ 62%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_32.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_32.cpp -[ 62%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_64.cpp.o +[ 38%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_64.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_64.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_64.cpp -[ 63%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_96.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_96.cpp -[ 64%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_96.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, @@ -3472,8 +2477,6 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: 'class gatb::core::tools::math::NativeInt8' declared here class NativeInt8 : private misc::ArrayData ^~~~~~~~~~ -[ 64%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_128.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, @@ -3495,6 +2498,8 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: 'class gatb::core::tools::math::NativeInt8' declared here class NativeInt8 : private misc::ArrayData ^~~~~~~~~~ +[ 39%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_96.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_96.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, @@ -3516,39 +2521,10 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: 'class gatb::core::tools::math::NativeInt8' declared here class NativeInt8 : private misc::ArrayData ^~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:6: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 96]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:14:16: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountFileNames.size(); ii++) - ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountFileNames.size(); ii++) - ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with unsigned int span = 96]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 96]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:14:16: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] - while(filenames.size() > _reduceTarget) - ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< currentFiles.size(); ii++) - ~~^~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< _tmpCountIterators.size(); ii++) -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii< currentFiles.size(); ii++) - ~~^~~~~~~~~~~~~~~~~~~~~ +[ 39%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_128.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp +[ 39%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_32.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, @@ -3564,121 +2540,8 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:311:21: warning: unused variable 'abundance' [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 96; Derived = gatb::core::kmer::impl::CountProcessorSoliditySum<96>]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - result.add (0, "kmers"); - ~~~~~~~~~~~^~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 96; Derived = gatb::core::kmer::impl::CountProcessorSolidityAll<96>]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 96; Derived = gatb::core::kmer::impl::CountProcessorSolidityCustom<96>]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 96; Derived = gatb::core::kmer::impl::CountProcessorSolidityOne<96>]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 96; Derived = gatb::core::kmer::impl::CountProcessorSolidityMax<96>]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 96; Derived = gatb::core::kmer::impl::CountProcessorSolidityMin<96>]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:28, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorDump::getProperties() const [with unsigned int span = 96]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:159:35: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:172:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - result.add (0, "partitions"); - ~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:27, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of 'void gatb::core::kmer::impl::CountProcessorHistogram::end() [with unsigned int span = 96]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:104:10: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:117:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=0; ii<= _histogram->getLength(); ii++) - ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:120:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] - for(int jj=0; jj<= _histogram->getLength2(); jj++) - ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:135:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] - for(int ii=1; ii<= _histogram->getLength(); ii++) - ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorHistogram::getProperties() const [with unsigned int span = 96]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:191:35: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:195:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - result.add (0, "histogram"); - ~~~~~~~~~~~^~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with unsigned int span = 96]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1057:5: required from 'void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with unsigned int span = 96; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<96>::SuperKmer]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1048:8: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] - while(uid<4 && skid < superKmerLen) - ~~~~~^~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] - if(skid >= superKmerLen) break; - ~~~~~^~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<96>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] - memset (_data, 0, _blockSize*sizeof(Item)); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<96>::Count' declared here - struct Count : tools::misc::Abundance - ^~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt64; size_t = unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt64]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class gatb::core::tools::math::NativeInt64'; use assignment or value-initialization instead [-Wclass-memaccess] - memset (_data, 0, _blockSize*sizeof(Item)); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/Integer.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: 'class gatb::core::tools::math::NativeInt64' declared here - class NativeInt64 - ^~~~~~~~~~~ -[ 64%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_32.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp -[ 64%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_128.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_128.cpp -[ 65%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_64.cpp.o +[ 40%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_64.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_64.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp -[ 65%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_96.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, @@ -3694,6 +2557,8 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:311:21: warning: unused variable 'abundance' [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ +[ 40%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_96.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, @@ -3703,8 +2568,6 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -[ 66%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_128.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:6: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of 'void gatb::core::kmer::impl::MPHFAlgorithm::check() [with unsigned int span = 64; Abundance_t = unsigned char; NodeState_t = unsigned char]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:13:16: required from here @@ -3720,35 +2583,14 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_128.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt8; size_t = unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt8]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class gatb::core::tools::math::NativeInt8'; use assignment or value-initialization instead [-Wclass-memaccess] - memset (_data, 0, _blockSize*sizeof(Item)); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_128.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: 'class gatb::core::tools::math::NativeInt8' declared here - class NativeInt8 : private misc::ArrayData - ^~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp:6: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of 'void gatb::core::kmer::impl::MPHFAlgorithm::check() [with unsigned int span = 96; Abundance_t = unsigned char; NodeState_t = unsigned char]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp:13:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:311:21: warning: unused variable 'abundance' [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ -[ 66%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_32.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp +[ 41%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_128.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, @@ -3760,100 +2602,16 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -[ 66%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_64.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_64.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:7: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] props->add (0, "host"); ^ -[ 67%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_96.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp -[ 67%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_32.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_32.cpp -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:7: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - props->add (0, "host"); - ^ -[ 68%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_64.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_64.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_64.cpp -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:7: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - props->add (0, "host"); - ^ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:7: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - props->add (0, "host"); - ^ -[ 68%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_96.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_96.cpp -[ 68%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_128.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_32.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt8; size_t = unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt8]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class gatb::core::tools::math::NativeInt8'; use assignment or value-initialization instead [-Wclass-memaccess] - memset (_data, 0, _blockSize*sizeof(Item)); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_32.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: 'class gatb::core::tools::math::NativeInt8' declared here - class NativeInt8 : private misc::ArrayData - ^~~~~~~~~~ -[ 69%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_32.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp -[ 70%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_128.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp +[ 41%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_32.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp +[ 41%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_64.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_64.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, @@ -3938,29 +2696,84 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<128>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ -[ 70%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_64.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_64.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_64.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt8; size_t = unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt8]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class gatb::core::tools::math::NativeInt8'; use assignment or value-initialization instead [-Wclass-memaccess] - memset (_data, 0, _blockSize*sizeof(Item)); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_64.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: 'class gatb::core::tools::math::NativeInt8' declared here - class NativeInt8 : private misc::ArrayData - ^~~~~~~~~~ +[ 42%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_96.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:7: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + props->add (0, "host"); + ^ +[ 42%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_128.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:7: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + props->add (0, "host"); + ^ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:7: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + props->add (0, "host"); + ^ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp:2: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp:2: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of 'bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >; Edge = gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >; Graph = gatb::core::debruijn::impl::GraphTemplate, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, boost::variant, gatb::core::debruijn::impl::GraphData<32>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<64>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<96>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<128>, boost::mpl::l_end> > > > > > >]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:852:16: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::set, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, std::less, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > >, std::allocator, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > > >::size_type' {aka 'unsigned int'} [-Wformat=] + if (debug) printf("%lu-bubble mean %d, stdev %.1f\n",consensuses.size(),mean,stdev); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of 'bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t >; Edge = gatb::core::debruijn::impl::Edge_t > >; Graph = gatb::core::debruijn::impl::GraphTemplate >, gatb::core::debruijn::impl::Edge_t > >, boost::variant > >]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp:18:16: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::set > >, std::less > > >, std::allocator > > > >::size_type' {aka 'unsigned int'} [-Wformat=] +[ 43%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_32.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, @@ -4024,18 +2837,6 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<64>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp:2: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, @@ -4057,8 +2858,8 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ -[ 70%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_32.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp +[ 43%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_64.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_64.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, @@ -4071,60 +2872,8 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp:2: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of 'bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >; Edge = gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >; Graph = gatb::core::debruijn::impl::GraphTemplate, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, boost::variant, gatb::core::debruijn::impl::GraphData<32>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<64>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<96>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<128>, boost::mpl::l_end> > > > > > >]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:852:16: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::set, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, std::less, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > >, std::allocator, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > > >::size_type' {aka 'unsigned int'} [-Wformat=] - if (debug) printf("%lu-bubble mean %d, stdev %.1f\n",consensuses.size(),mean,stdev); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:6: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of 'bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t >; Edge = gatb::core::debruijn::impl::Edge_t > >; Graph = gatb::core::debruijn::impl::GraphTemplate >, gatb::core::debruijn::impl::Edge_t > >, boost::variant > >]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp:18:16: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::set > >, std::less > > >, std::allocator > > > >::size_type' {aka 'unsigned int'} [-Wformat=] -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_96.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt8; size_t = unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt8]' -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class gatb::core::tools::math::NativeInt8'; use assignment or value-initialization instead [-Wclass-memaccess] - memset (_data, 0, _blockSize*sizeof(Item)); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_96.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: 'class gatb::core::tools::math::NativeInt8' declared here - class NativeInt8 : private misc::ArrayData - ^~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:6: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of 'void gatb::core::kmer::impl::MPHFAlgorithm::check() [with unsigned int span = 128; Abundance_t = unsigned char; NodeState_t = unsigned char]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:13:16: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:311:21: warning: unused variable 'abundance' [-Wunused-variable] - Abundance_t abundance = (*_abundanceMap)[count.value]; - ^~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp:2: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of 'bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >; Edge = gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >; Graph = gatb::core::debruijn::impl::GraphTemplate, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, boost::variant, gatb::core::debruijn::impl::GraphData<32>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<64>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<96>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<128>, boost::mpl::l_end> > > > > > >]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:852:16: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::set, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, std::less, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > >, std::allocator, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > > >::size_type' {aka 'unsigned int'} [-Wformat=] - if (debug) printf("%lu-bubble mean %d, stdev %.1f\n",consensuses.size(),mean,stdev); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of 'bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t >; Edge = gatb::core::debruijn::impl::Edge_t > >; Graph = gatb::core::debruijn::impl::GraphTemplate >, gatb::core::debruijn::impl::Edge_t > >, boost::variant > >]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp:18:16: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::set > >, std::less > > >, std::allocator > > > >::size_type' {aka 'unsigned int'} [-Wformat=] +[ 43%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_96.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_96.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, @@ -4188,18 +2937,6 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp:2: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, @@ -4221,15 +2958,15 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<64>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp:2: +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of 'bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >; Edge = gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >; Graph = gatb::core::debruijn::impl::GraphTemplate, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, boost::variant, gatb::core::debruijn::impl::GraphData<32>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<64>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<96>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<128>, boost::mpl::l_end> > > > > > >]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:852:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::set, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, std::less, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > >, std::allocator, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > > >::size_type' {aka 'unsigned int'} [-Wformat=] if (debug) printf("%lu-bubble mean %d, stdev %.1f\n",consensuses.size(),mean,stdev); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of 'bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t >; Edge = gatb::core::debruijn::impl::Edge_t > >; Graph = gatb::core::debruijn::impl::GraphTemplate >, gatb::core::debruijn::impl::Edge_t > >, boost::variant > >]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp:18:16: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::set > >, std::less > > >, std::allocator > > > >::size_type' {aka 'unsigned int'} [-Wformat=] +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of 'bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t >; Edge = gatb::core::debruijn::impl::Edge_t > >; Graph = gatb::core::debruijn::impl::GraphTemplate >, gatb::core::debruijn::impl::Edge_t > >, boost::variant > >]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp:18:16: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::set > >, std::less > > >, std::allocator > > > >::size_type' {aka 'unsigned int'} [-Wformat=] In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, @@ -4317,22 +3054,15 @@ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:6: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:6: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of 'void gatb::core::kmer::impl::MPHFAlgorithm::check() [with unsigned int span = 32; Abundance_t = unsigned char; NodeState_t = unsigned char]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:13:16: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:311:21: warning: unused variable 'abundance' [-Wunused-variable] - Abundance_t abundance = (*_abundanceMap)[count.value]; - ^~~~~~~~~ -[ 70%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_96.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_96.cpp -[ 71%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_128.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, @@ -4345,21 +3075,26 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -[ 71%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_64.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_64.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp -[ 71%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_32.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp:2: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of 'bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >; Edge = gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >; Graph = gatb::core::debruijn::impl::GraphTemplate, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, boost::variant, gatb::core::debruijn::impl::GraphData<32>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<64>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<96>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<128>, boost::mpl::l_end> > > > > > >]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:852:16: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::set, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, std::less, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > >, std::allocator, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > > >::size_type' {aka 'unsigned int'} [-Wformat=] + if (debug) printf("%lu-bubble mean %d, stdev %.1f\n",consensuses.size(),mean,stdev); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of 'bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t >; Edge = gatb::core::debruijn::impl::Edge_t > >; Graph = gatb::core::debruijn::impl::GraphTemplate >, gatb::core::debruijn::impl::Edge_t > >, boost::variant > >]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp:18:16: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::set > >, std::less > > >, std::allocator > > > >::size_type' {aka 'unsigned int'} [-Wformat=] In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_96.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of 'bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >; Edge = gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >; Graph = gatb::core::debruijn::impl::GraphTemplate, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, boost::variant, gatb::core::debruijn::impl::GraphData<32>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<64>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<96>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<128>, boost::mpl::l_end> > > > > > >]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:852:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::set, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, std::less, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > >, std::allocator, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > > >::size_type' {aka 'unsigned int'} [-Wformat=] if (debug) printf("%lu-bubble mean %d, stdev %.1f\n",consensuses.size(),mean,stdev); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 72%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_96.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of 'bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t >; Edge = gatb::core::debruijn::impl::Edge_t > >; Graph = gatb::core::debruijn::impl::GraphTemplate >, gatb::core::debruijn::impl::Edge_t > >, boost::variant > >]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_96.cpp:18:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::set > >, std::less > > >, std::allocator > > > >::size_type' {aka 'unsigned int'} [-Wformat=] +[ 44%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_128.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, @@ -4371,108 +3106,12 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -[ 72%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_128.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] props->add (0, "host"); ^ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:6: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp:6: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:6: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of 'void gatb::core::kmer::impl::MPHFAlgorithm::check() [with unsigned int span = 64; Abundance_t = unsigned char; NodeState_t = unsigned char]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:13:16: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:311:21: warning: unused variable 'abundance' [-Wunused-variable] - Abundance_t abundance = (*_abundanceMap)[count.value]; - ^~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:2: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - props->add (0, "host"); - ^ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp:6: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of 'void gatb::core::kmer::impl::MPHFAlgorithm::check() [with unsigned int span = 96; Abundance_t = unsigned char; NodeState_t = unsigned char]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp:13:16: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:311:21: warning: unused variable 'abundance' [-Wunused-variable] - Abundance_t abundance = (*_abundanceMap)[count.value]; - ^~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:7: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - props->add (0, "host"); - ^ -[ 73%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_64.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_64.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp -[ 73%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_96.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp -[ 75%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_32.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp -[ 75%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_128.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_128.cpp -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, @@ -4557,13 +3196,36 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ +[ 44%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_32.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:2: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + props->add (0, "host"); + ^ +[ 45%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_64.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_64.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp +[ 45%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_96.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); @@ -4574,6 +3236,19 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] props->add (0, "host"); ^ +[ 45%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_128.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_128.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': @@ -4601,12 +3276,6 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<128>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:7: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - props->add (0, "host"); - ^ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, @@ -4687,16 +3356,35 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] props->add (0, "host"); ^ -[ 75%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_64.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_64.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<128>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] + memset (_data, 0, _blockSize*sizeof(Item)); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<128>::Count' declared here + struct Count : tools::misc::Abundance + ^~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = unsigned int]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here @@ -4704,9 +3392,9 @@ memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<96>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ @@ -4715,9 +3403,9 @@ from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = unsigned int]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here @@ -4725,9 +3413,9 @@ memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<64>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ @@ -4736,9 +3424,9 @@ from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = unsigned int]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here @@ -4746,9 +3434,9 @@ memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ @@ -4757,9 +3445,9 @@ from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = unsigned int]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here @@ -4767,135 +3455,1030 @@ memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<128>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ -[ 76%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_96.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp -[ 76%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_128.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<96>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] + memset (_data, 0, _blockSize*sizeof(Item)); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<96>::Count' declared here + struct Count : tools::misc::Abundance + ^~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<64>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] + memset (_data, 0, _blockSize*sizeof(Item)); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<64>::Count' declared here + struct Count : tools::misc::Abundance + ^~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] + memset (_data, 0, _blockSize*sizeof(Item)); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<>::Count' declared here + struct Count : tools::misc::Abundance + ^~~~~ +[ 45%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/GraphUnitigs.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/GraphUnitigs.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.hpp:27, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:31: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + props->add (0, "host"); + ^ +[ 46%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/IterativeExtensions.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/IterativeExtensions.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:7: +[ 46%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/LinkTigs.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/LinkTigs.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/LinkTigs.cpp +[ 47%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Simplifications.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Simplifications.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +[ 48%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_32.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_32.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_32.cpp:1: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:31, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_32.cpp:3: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] props->add (0, "host"); ^ -[ 77%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_32.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_32.cpp -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:7: +[ 48%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Terminator.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Terminator.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.cpp:24: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +[ 48%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Traversal.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Traversal.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of 'bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >; Edge = gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >; Graph = gatb::core::debruijn::impl::GraphTemplate, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, boost::variant, gatb::core::debruijn::impl::GraphData<32>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<64>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<96>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<128>, boost::mpl::l_end> > > > > > >]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:852:16: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::set, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, std::less, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > >, std::allocator, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > > >::size_type' {aka 'unsigned int'} [-Wformat=] + if (debug) printf("%lu-bubble mean %d, stdev %.1f\n",consensuses.size(),mean,stdev); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 50%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp +[ 50%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/BloomAlgorithm.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/BloomAlgorithm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp +[ 50%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_64.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_64.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_64.cpp +[ 51%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/BloomBuilder.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/BloomBuilder.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomBuilder.cpp +[ 51%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/Configuration.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/Configuration.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Configuration.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_64.cpp:1: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:31, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_64.cpp:3: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] props->add (0, "host"); ^ -[ 77%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_32.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp +[ 51%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/ConfigurationAlgorithm.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/ConfigurationAlgorithm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/ConfigurationAlgorithm.cpp +[ 52%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/DebloomAlgorithm.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/DebloomAlgorithm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/DebloomAlgorithm.cpp +[ 52%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp +[ 53%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/LinearCounter.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/LinearCounter.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/LinearCounter.cpp +[ 53%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/MPHFAlgorithm.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/MPHFAlgorithm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp +[ 53%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/Model.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/Model.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +[ 54%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/ModelData.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/ModelData.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/ModelData.cpp +[ 54%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/PartiInfo.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/PartiInfo.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp +[ 55%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_96.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_96.cpp +[ 55%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_128.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_128.cpp +[ 55%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_32.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_32.cpp +[ 56%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_64.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_64.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_64.cpp +[ 56%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_96.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_96.cpp +[ 57%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/PartitionsCommand.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/PartitionsCommand.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp: In member function 'void gatb::core::kmer::impl::Repartitor::printInfo()': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp:308:12: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'size_t' {aka 'unsigned int'} [-Wformat=] + printf("Repartitor : nbMinimizers=%ld\n", nbMinimizers); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp:309:61: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'u_int64_t' {aka 'long long unsigned int'} [-Wformat=] + for (u_int64_t ii=0; ii::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:31, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_96.cpp:3: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + props->add (0, "host"); + ^ +[ 57%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/SortingCountAlgorithm.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/SortingCountAlgorithm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp +[ 58%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemCommon.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemCommon.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/FileSystemCommon.cpp +[ 58%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemLinux.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemLinux.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/FileSystemLinux.cpp +[ 59%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemMacos.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemMacos.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/FileSystemMacos.cpp +[ 59%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/System.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/System.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/System.cpp +[ 59%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/SystemInfoCommon.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/SystemInfoCommon.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/SystemInfoCommon.cpp +[ 60%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/ThreadLinux.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/ThreadLinux.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/ThreadLinux.cpp +[ 60%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/ThreadMacos.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/ThreadMacos.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/ThreadMacos.cpp +[ 61%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/collections/impl/Bloom.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/collections/impl/Bloom.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/Bloom.cpp +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/ThreadLinux.cpp: In constructor 'gatb::core::system::impl::ThreadLinux::ThreadLinux(void* (*)(void*), void*)': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/ThreadLinux.cpp:51:7: warning: variable 'ret' set but not used [-Wunused-but-set-variable] + int ret = pthread_attr_init ( &tattr ) ; + ^~~ +[ 61%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/DnaCoder.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/DnaCoder.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.cpp +[ 61%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/HeaderCoder.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/HeaderCoder.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp +[ 62%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/Leon.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/Leon.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp +[ 62%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/RangeCoder.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/RangeCoder.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/RangeCoder.cpp +[ 63%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/designpattern/impl/Command.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/designpattern/impl/Command.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.cpp:21: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.hpp:35, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:21: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp: In member function 'void Leon::createBloom()': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:323:47: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + getInfo()->add (0, "Abundance threshold"); + ^ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:328:49: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + getInfo()->add (0, "Abundance threshold"); + ^ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp: In member function 'void Leon::executeCompression()': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:404:43: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + getInfo()->add (0, "Input format: FastQ"); + ^ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:410:66: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + getInfo()->add (0, "Quality compression: LOSSLESS mode"); + ^ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:412:106: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + getInfo()->add (0, "Quality compression: lossy mode (use '-lossless' for lossless compression)"); + ^ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:422:43: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + getInfo()->add (0, "Input format: FastA"); + ^ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:429:123: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + getInfo()->add (0, "Input format: unknown. Input extension must be one among fasta (.fa, .fasta) or fastq (.fq, .fastq)"); + ^ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp: In member function 'void Leon::endCompression()': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:727:40: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + getInfo()->add(0, "End compression"); + ^ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp: In member function 'void Leon::endHeaderCompression()': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:883:44: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + getInfo()->add(0, "End Header compression"); + ^ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp: In member function 'void Leon::endDnaCompression()': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:970:47: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + getInfo()->add(0, "End Sequence compression"); + ^ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp: In member function 'void Leon::executeDecompression()': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:1429:38: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + getInfo()->add(0, "Decompression"); + ^ +[ 63%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/designpattern/impl/Observer.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/designpattern/impl/Observer.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Observer.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.cpp:21: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt8; size_t = unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt8]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class gatb::core::tools::math::NativeInt8'; use assignment or value-initialization instead [-Wclass-memaccess] + memset (_data, 0, _blockSize*sizeof(Item)); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.cpp:21: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: 'class gatb::core::tools::math::NativeInt8' declared here + class NativeInt8 : private misc::ArrayData + ^~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.hpp:35, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:21: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt8; size_t = unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt8]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class gatb::core::tools::math::NativeInt8'; use assignment or value-initialization instead [-Wclass-memaccess] + memset (_data, 0, _blockSize*sizeof(Item)); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.hpp:35, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:21: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: 'class gatb::core::tools::math::NativeInt8' declared here + class NativeInt8 : private misc::ArrayData + ^~~~~~~~~~ +[ 63%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/api/Data.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/api/Data.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/api/Data.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] + memset (_data, 0, _blockSize*sizeof(Item)); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:71, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<>::Count' declared here + struct Count : tools::misc::Abundance + ^~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt8; size_t = unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt8]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class gatb::core::tools::math::NativeInt8'; use assignment or value-initialization instead [-Wclass-memaccess] + memset (_data, 0, _blockSize*sizeof(Item)); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: 'class gatb::core::tools::math::NativeInt8' declared here + class NativeInt8 : private misc::ArrayData + ^~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt64; size_t = unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt64]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class gatb::core::tools::math::NativeInt64'; use assignment or value-initialization instead [-Wclass-memaccess] + memset (_data, 0, _blockSize*sizeof(Item)); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:40, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: 'class gatb::core::tools::math::NativeInt64' declared here + class NativeInt64 + ^~~~~~~~~~~ +[ 64%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Algorithm.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Algorithm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.cpp +[ 64%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Histogram.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Histogram.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Histogram.cpp +[ 65%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/OptionsParser.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/OptionsParser.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/OptionsParser.cpp +[ 65%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Progress.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Progress.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp: In member function 'virtual void gatb::core::tools::misc::impl::ProgressTimerAndSystem::fillBuffer(double)': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp:350:33: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'u_int64_t' {aka 'long long unsigned int'} [-Wformat=] + snprintf (tmp, sizeof(tmp), " cpu: %5.1f %% mem: [%4lu, %4lu, %4lu] MB ", + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp:352:9: + mem, _memMax, memMaxProcess + ~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp:350:33: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'u_int64_t' {aka 'long long unsigned int'} [-Wformat=] +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp:350:33: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'u_int64_t' {aka 'long long unsigned int'} [-Wformat=] +[ 65%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Property.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Property.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp +[ 66%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/TimeInfo.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/TimeInfo.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/TimeInfo.cpp +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp: In member function 'virtual void gatb::core::tools::misc::impl::Properties::setInt(const string&, const int64_t&)': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp:438:39: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] + snprintf (buffer, sizeof(buffer), "%ld", value); + ^~~~~ ~~~~~ +[ 66%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Tokenizer.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Tokenizer.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Tokenizer.cpp +[ 67%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Tool.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Tool.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Tool.cpp +[ 67%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/XmlReader.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/XmlReader.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/XmlReader.cpp +[ 67%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/storage/impl/Storage.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/storage/impl/Storage.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.cpp +[ 68%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/storage/impl/StorageTools.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/storage/impl/StorageTools.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageTools.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.cpp:22: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt8; size_t = unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt8]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class gatb::core::tools::math::NativeInt8'; use assignment or value-initialization instead [-Wclass-memaccess] + memset (_data, 0, _blockSize*sizeof(Item)); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.cpp:22: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: 'class gatb::core::tools::math::NativeInt8' declared here + class NativeInt8 : private misc::ArrayData + ^~~~~~~~~~ +[ 68%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_128.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp +[ 69%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_32.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp +[ 69%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_64.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_64.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp +[ 69%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_96.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_96.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with unsigned int span = 128]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp:13:17: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] + while(uid<4 && skid < superKmerLen) + ~~~~~^~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] + if(skid >= superKmerLen) break; + ~~~~~^~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with unsigned int span = 32]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp:13:17: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] + while(uid<4 && skid < superKmerLen) + ~~~~~^~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] + if(skid >= superKmerLen) break; + ~~~~~^~~~~~~~~~~~~~~ +[ 70%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_128.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with unsigned int span = 64]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp:13:17: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] + while(uid<4 && skid < superKmerLen) + ~~~~~^~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] + if(skid >= superKmerLen) break; + ~~~~~^~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_96.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with unsigned int span = 96]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_96.cpp:13:17: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] + while(uid<4 && skid < superKmerLen) + ~~~~~^~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] + if(skid >= superKmerLen) break; + ~~~~~^~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:2: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +[ 70%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_32.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp +[ 71%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_64.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_64.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:3: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In instantiation of 'void gatb::core::debruijn::impl::graph3::debruijn() [with unsigned int span = 128]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:31:16: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:236:10: warning: unused variable 'debug_index' [-Wunused-variable] + uint debug_index = 0; + ^~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:2: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of 'uint64_t boomphf::mphf::totalBitSize() [with elem_t = long long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long long unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:765:60: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with unsigned int SPAN = 128; std::__cxx11::string = std::__cxx11::basic_string]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:29:9: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::unordered_map, std::equal_to, std::allocator > >::size_type' {aka 'unsigned int'} [-Wformat=] + printf("final hash %12lu bits (%.2f %%) (nb in final hash %lu)\n", + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::unordered_map, std::equal_to, std::allocator > >::size_type' {aka 'unsigned int'} [-Wformat=] +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:2: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp: In instantiation of 'void gatb::core::debruijn::impl::determine_order_sequences(std::vector >&, const std::vector >&, int, bool) [with int SPAN = 128]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:1106:48: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with unsigned int SPAN = 128; std::__cxx11::string = std::__cxx11::basic_string]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:29:9: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:258:18: warning: unused variable 'first_index' [-Wunused-variable] + uint32_t first_index = markedSequence_index; + ^~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = unsigned int]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<128>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.h:15, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<128>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:2: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:2: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:3: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In instantiation of 'void gatb::core::debruijn::impl::graph3::debruijn() [with unsigned int span = 32]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:31:16: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:236:10: warning: unused variable 'debug_index' [-Wunused-variable] + uint debug_index = 0; + ^~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:3: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In instantiation of 'void gatb::core::debruijn::impl::graph3::debruijn() [with unsigned int span = 64]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:31:16: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:236:10: warning: unused variable 'debug_index' [-Wunused-variable] + uint debug_index = 0; + ^~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:2: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of 'uint64_t boomphf::mphf::totalBitSize() [with elem_t = long long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long long unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:765:60: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with unsigned int SPAN = 32; std::__cxx11::string = std::__cxx11::basic_string]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:29:9: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::unordered_map, std::equal_to, std::allocator > >::size_type' {aka 'unsigned int'} [-Wformat=] + printf("final hash %12lu bits (%.2f %%) (nb in final hash %lu)\n", + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::unordered_map, std::equal_to, std::allocator > >::size_type' {aka 'unsigned int'} [-Wformat=] +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:2: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp: In instantiation of 'void gatb::core::debruijn::impl::determine_order_sequences(std::vector >&, const std::vector >&, int, bool) [with int SPAN = 32]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:1106:48: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with unsigned int SPAN = 32; std::__cxx11::string = std::__cxx11::basic_string]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:29:9: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:258:18: warning: unused variable 'first_index' [-Wunused-variable] + uint32_t first_index = markedSequence_index; + ^~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:2: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of 'uint64_t boomphf::mphf::totalBitSize() [with elem_t = long long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long long unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:765:60: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with unsigned int SPAN = 64; std::__cxx11::string = std::__cxx11::basic_string]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:29:9: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::unordered_map, std::equal_to, std::allocator > >::size_type' {aka 'unsigned int'} [-Wformat=] + printf("final hash %12lu bits (%.2f %%) (nb in final hash %lu)\n", + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::unordered_map, std::equal_to, std::allocator > >::size_type' {aka 'unsigned int'} [-Wformat=] +[ 72%] Linking CXX static library ../lib/None/libgatbcore.a +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/gatbcore-static.dir/cmake_clean_target.cmake +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:2: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp: In instantiation of 'void gatb::core::debruijn::impl::determine_order_sequences(std::vector >&, const std::vector >&, int, bool) [with int SPAN = 64]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:1106:48: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with unsigned int SPAN = 64; std::__cxx11::string = std::__cxx11::basic_string]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:29:9: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:258:18: warning: unused variable 'first_index' [-Wunused-variable] + uint32_t first_index = markedSequence_index; + ^~~~~~~~~~~ +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/gatbcore-static.dir/link.txt --verbose=1 +/usr/bin/ar qc ../lib/None/libgatbcore.a CMakeFiles/gatbcore-static.dir/gatb/bank/impl/Bank.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankAlbum.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankBinary.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankFasta.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankHelpers.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankRandom.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankSplitter.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bcalm2/bcalm_algo.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bcalm2/bglue_algo.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bcalm2/logging.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bcalm2/ograph.cpp.o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/BranchingAlgorithm.cpp.o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Frontline.cpp.o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Graph.cpp.o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/GraphUnitigs.cpp.o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/IterativeExtensions.cpp.o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/LinkTigs.cpp.o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Simplifications.cpp.o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Terminator.cpp.o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Traversal.cpp.o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp.o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/BloomAlgorithm.cpp.o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/BloomBuilder.cpp.o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/Configuration.cpp.o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/ConfigurationAlgorithm.cpp.o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/DebloomAlgorithm.cpp.o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp.o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/LinearCounter.cpp.o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/MPHFAlgorithm.cpp.o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/Model.cpp.o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/ModelData.cpp.o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/PartiInfo.cpp.o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/PartitionsCommand.cpp.o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/RepartitionAlgorithm.cpp.o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/SortingCountAlgorithm.cpp.o CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemCommon.cpp.o CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemLinux.cpp.o CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemMacos.cpp.o CMakeFiles/gatbcore-static.dir/gatb/system/impl/System.cpp.o CMakeFiles/gatbcore-static.dir/gatb/system/impl/SystemInfoCommon.cpp.o CMakeFiles/gatbcore-static.dir/gatb/system/impl/ThreadLinux.cpp.o CMakeFiles/gatbcore-static.dir/gatb/system/impl/ThreadMacos.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/collections/impl/Bloom.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/compression/DnaCoder.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/compression/HeaderCoder.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/compression/Leon.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/compression/RangeCoder.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/designpattern/impl/Command.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/designpattern/impl/Observer.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/api/Data.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Algorithm.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Histogram.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/OptionsParser.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Progress.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Property.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/TimeInfo.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Tokenizer.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Tool.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/XmlReader.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/storage/impl/Storage.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/storage/impl/StorageTools.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_96.cpp.o In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]' + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:1: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<32>::Count; size_t = unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<32>::Count]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<96>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<32>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<96>::Count' declared here +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.h:15, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:1: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<32>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = unsigned int]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<64>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.h:15, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<64>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ +[ 72%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_96.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp +[ 72%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_128.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp +[ 73%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_32.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp +[ 73%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_64.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_64.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:6: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 128]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:14:16: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountFileNames.size(); ii++) + ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountFileNames.size(); ii++) + ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with unsigned int span = 128]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 128]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:14:16: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] + while(filenames.size() > _reduceTarget) + ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< currentFiles.size(); ii++) + ~~^~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< currentFiles.size(); ii++) + ~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:3: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In instantiation of 'void gatb::core::debruijn::impl::graph3::debruijn() [with unsigned int span = 96]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:31:16: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:236:10: warning: unused variable 'debug_index' [-Wunused-variable] + uint debug_index = 0; + ^~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 128; Derived = gatb::core::kmer::impl::CountProcessorSoliditySum<128>]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + result.add (0, "kmers"); + ~~~~~~~~~~~^~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 128; Derived = gatb::core::kmer::impl::CountProcessorSolidityAll<128>]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 128; Derived = gatb::core::kmer::impl::CountProcessorSolidityCustom<128>]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 128; Derived = gatb::core::kmer::impl::CountProcessorSolidityOne<128>]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 128; Derived = gatb::core::kmer::impl::CountProcessorSolidityMax<128>]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 128; Derived = gatb::core::kmer::impl::CountProcessorSolidityMin<128>]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:28, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorDump::getProperties() const [with unsigned int span = 128]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:159:35: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:172:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + result.add (0, "partitions"); + ~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:27, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of 'void gatb::core::kmer::impl::CountProcessorHistogram::end() [with unsigned int span = 128]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:104:10: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:117:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii<= _histogram->getLength(); ii++) + ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:120:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] + for(int jj=0; jj<= _histogram->getLength2(); jj++) + ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:135:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=1; ii<= _histogram->getLength(); ii++) + ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorHistogram::getProperties() const [with unsigned int span = 128]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:191:35: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:195:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + result.add (0, "histogram"); + ~~~~~~~~~~~^~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with unsigned int span = 128]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1057:5: required from 'void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with unsigned int span = 128; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<128>::SuperKmer]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1048:8: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] + while(uid<4 && skid < superKmerLen) + ~~~~~^~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] + if(skid >= superKmerLen) break; + ~~~~~^~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of 'uint64_t boomphf::mphf::totalBitSize() [with elem_t = long long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long long unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:765:60: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with unsigned int SPAN = 96; std::__cxx11::string = std::__cxx11::basic_string]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:29:9: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::unordered_map, std::equal_to, std::allocator > >::size_type' {aka 'unsigned int'} [-Wformat=] + printf("final hash %12lu bits (%.2f %%) (nb in final hash %lu)\n", + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::unordered_map, std::equal_to, std::allocator > >::size_type' {aka 'unsigned int'} [-Wformat=] +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp: In instantiation of 'void gatb::core::debruijn::impl::determine_order_sequences(std::vector >&, const std::vector >&, int, bool) [with int SPAN = 96]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:1106:48: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with unsigned int SPAN = 96; std::__cxx11::string = std::__cxx11::basic_string]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:29:9: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:258:18: warning: unused variable 'first_index' [-Wunused-variable] + uint32_t first_index = markedSequence_index; + ^~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:6: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 32]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:14:16: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountFileNames.size(); ii++) + ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountFileNames.size(); ii++) + ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<128>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] + memset (_data, 0, _blockSize*sizeof(Item)); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<128>::Count' declared here + struct Count : tools::misc::Abundance + ^~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt64; size_t = unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt64]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class gatb::core::tools::math::NativeInt64'; use assignment or value-initialization instead [-Wclass-memaccess] + memset (_data, 0, _blockSize*sizeof(Item)); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/Integer.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: 'class gatb::core::tools::math::NativeInt64' declared here + class NativeInt64 + ^~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with unsigned int span = 32]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 32]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:14:16: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] + while(filenames.size() > _reduceTarget) + ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< currentFiles.size(); ii++) + ~~^~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< currentFiles.size(); ii++) + ~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 32; Derived = gatb::core::kmer::impl::CountProcessorSoliditySum<32>]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + result.add (0, "kmers"); + ~~~~~~~~~~~^~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 32; Derived = gatb::core::kmer::impl::CountProcessorSolidityAll<32>]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 32; Derived = gatb::core::kmer::impl::CountProcessorSolidityCustom<32>]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 32; Derived = gatb::core::kmer::impl::CountProcessorSolidityOne<32>]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 32; Derived = gatb::core::kmer::impl::CountProcessorSolidityMax<32>]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 32; Derived = gatb::core::kmer::impl::CountProcessorSolidityMin<32>]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:6: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 64]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:14:16: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountFileNames.size(); ii++) + ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:28, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorDump::getProperties() const [with unsigned int span = 32]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:159:35: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:172:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + result.add (0, "partitions"); + ~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:27, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of 'void gatb::core::kmer::impl::CountProcessorHistogram::end() [with unsigned int span = 32]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:104:10: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:117:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii<= _histogram->getLength(); ii++) + ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:120:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] + for(int jj=0; jj<= _histogram->getLength2(); jj++) + ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:135:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=1; ii<= _histogram->getLength(); ii++) + ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorHistogram::getProperties() const [with unsigned int span = 32]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:191:35: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:195:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + result.add (0, "histogram"); + ~~~~~~~~~~~^~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountFileNames.size(); ii++) + ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with unsigned int span = 32]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1057:5: required from 'void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with unsigned int span = 32; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<>::SuperKmer]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1048:8: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] + while(uid<4 && skid < superKmerLen) + ~~~~~^~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] + if(skid >= superKmerLen) break; + ~~~~~^~~~~~~~~~~~~~~ +[ 75%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_96.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with unsigned int span = 64]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 64]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:14:16: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] + while(filenames.size() > _reduceTarget) + ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< currentFiles.size(); ii++) + ~~^~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< currentFiles.size(); ii++) + ~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = unsigned int]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ @@ -4903,62 +4486,124 @@ from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]' + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt64; size_t = unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt64]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<128>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class gatb::core::tools::math::NativeInt64'; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<128>::Count' declared here - struct Count : tools::misc::Abundance - ^~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/Integer.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: 'class gatb::core::tools::math::NativeInt64' declared here + class NativeInt64 + ^~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = unsigned int]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<96>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.h:15, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<96>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 64; Derived = gatb::core::kmer::impl::CountProcessorSoliditySum<64>]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + result.add (0, "kmers"); + ~~~~~~~~~~~^~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 64; Derived = gatb::core::kmer::impl::CountProcessorSolidityAll<64>]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 64; Derived = gatb::core::kmer::impl::CountProcessorSolidityCustom<64>]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 64; Derived = gatb::core::kmer::impl::CountProcessorSolidityOne<64>]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 64; Derived = gatb::core::kmer::impl::CountProcessorSolidityMax<64>]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 64; Derived = gatb::core::kmer::impl::CountProcessorSolidityMin<64>]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:28, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorDump::getProperties() const [with unsigned int span = 64]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:159:35: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:172:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + result.add (0, "partitions"); + ~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:27, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of 'void gatb::core::kmer::impl::CountProcessorHistogram::end() [with unsigned int span = 64]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:104:10: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:117:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii<= _histogram->getLength(); ii++) + ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:120:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] + for(int jj=0; jj<= _histogram->getLength2(); jj++) + ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:135:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=1; ii<= _histogram->getLength(); ii++) + ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorHistogram::getProperties() const [with unsigned int span = 64]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:191:35: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:195:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + result.add (0, "histogram"); + ~~~~~~~~~~~^~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with unsigned int span = 64]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1057:5: required from 'void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with unsigned int span = 64; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<64>::SuperKmer]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1048:8: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] + while(uid<4 && skid < superKmerLen) + ~~~~~^~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] + if(skid >= superKmerLen) break; + ~~~~~^~~~~~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = unsigned int]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<64>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<64>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ @@ -4966,135 +4611,356 @@ from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]' + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt64; size_t = unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt64]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class gatb::core::tools::math::NativeInt64'; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<>::Count' declared here - struct Count : tools::misc::Abundance - ^~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/Integer.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: 'class gatb::core::tools::math::NativeInt64' declared here + class NativeInt64 + ^~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:6: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 96]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:14:16: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountFileNames.size(); ii++) + ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountFileNames.size(); ii++) + ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with unsigned int span = 96]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 96]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:14:16: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] + while(filenames.size() > _reduceTarget) + ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< currentFiles.size(); ii++) + ~~^~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< _tmpCountIterators.size(); ii++) +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii< currentFiles.size(); ii++) + ~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 96; Derived = gatb::core::kmer::impl::CountProcessorSoliditySum<96>]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + result.add (0, "kmers"); + ~~~~~~~~~~~^~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 96; Derived = gatb::core::kmer::impl::CountProcessorSolidityAll<96>]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 96; Derived = gatb::core::kmer::impl::CountProcessorSolidityCustom<96>]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 96; Derived = gatb::core::kmer::impl::CountProcessorSolidityOne<96>]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 96; Derived = gatb::core::kmer::impl::CountProcessorSolidityMax<96>]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 96; Derived = gatb::core::kmer::impl::CountProcessorSolidityMin<96>]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:28, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorDump::getProperties() const [with unsigned int span = 96]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:159:35: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:172:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + result.add (0, "partitions"); + ~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:27, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of 'void gatb::core::kmer::impl::CountProcessorHistogram::end() [with unsigned int span = 96]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:104:10: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:117:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=0; ii<= _histogram->getLength(); ii++) + ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:120:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] + for(int jj=0; jj<= _histogram->getLength2(); jj++) + ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:135:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] + for(int ii=1; ii<= _histogram->getLength(); ii++) + ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of 'gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorHistogram::getProperties() const [with unsigned int span = 96]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:191:35: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:195:20: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + result.add (0, "histogram"); + ~~~~~~~~~~~^~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with unsigned int span = 96]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1057:5: required from 'void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with unsigned int span = 96; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<96>::SuperKmer]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1048:8: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] + while(uid<4 && skid < superKmerLen) + ~~~~~^~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] + if(skid >= superKmerLen) break; + ~~~~~^~~~~~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]' + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<128>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<96>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<128>::Count' declared here +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<96>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]' + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt64; size_t = unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt64]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<96>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class gatb::core::tools::math::NativeInt64'; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<96>::Count' declared here - struct Count : tools::misc::Abundance - ^~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/Integer.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: 'class gatb::core::tools::math::NativeInt64' declared here + class NativeInt64 + ^~~~~~~~~~~ +[ 75%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_128.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_128.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]' + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_128.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt8; size_t = unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt8]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<64>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class gatb::core::tools::math::NativeInt8'; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<64>::Count' declared here - struct Count : tools::misc::Abundance - ^~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_128.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: 'class gatb::core::tools::math::NativeInt8' declared here + class NativeInt8 : private misc::ArrayData + ^~~~~~~~~~ +[ 75%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_32.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_32.cpp +[ 76%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_64.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_64.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_64.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]' + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_32.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt8; size_t = unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt8]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class gatb::core::tools::math::NativeInt8'; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<>::Count' declared here - struct Count : tools::misc::Abundance - ^~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_32.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: 'class gatb::core::tools::math::NativeInt8' declared here + class NativeInt8 : private misc::ArrayData + ^~~~~~~~~~ +[ 76%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_96.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_96.cpp +[ 77%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_128.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_64.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt8; size_t = unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt8]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class gatb::core::tools::math::NativeInt8'; use assignment or value-initialization instead [-Wclass-memaccess] + memset (_data, 0, _blockSize*sizeof(Item)); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_64.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: 'class gatb::core::tools::math::NativeInt8' declared here + class NativeInt8 : private misc::ArrayData + ^~~~~~~~~~ +/usr/bin/ranlib ../lib/None/libgatbcore.a +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:6: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:6: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of 'void gatb::core::kmer::impl::MPHFAlgorithm::check() [with unsigned int span = 128; Abundance_t = unsigned char; NodeState_t = unsigned char]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:13:16: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:311:21: warning: unused variable 'abundance' [-Wunused-variable] + Abundance_t abundance = (*_abundanceMap)[count.value]; + ^~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_96.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt8; size_t = unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt8]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class gatb::core::tools::math::NativeInt8'; use assignment or value-initialization instead [-Wclass-memaccess] + memset (_data, 0, _blockSize*sizeof(Item)); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_96.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: 'class gatb::core::tools::math::NativeInt8' declared here + class NativeInt8 : private misc::ArrayData + ^~~~~~~~~~ +[ 77%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_32.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:6: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:6: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of 'void gatb::core::kmer::impl::MPHFAlgorithm::check() [with unsigned int span = 32; Abundance_t = unsigned char; NodeState_t = unsigned char]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:13:16: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:311:21: warning: unused variable 'abundance' [-Wunused-variable] + Abundance_t abundance = (*_abundanceMap)[count.value]; + ^~~~~~~~~ +[ 77%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_64.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_64.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp +[ 78%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_96.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp +[ 78%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_128.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:6: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:6: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of 'void gatb::core::kmer::impl::MPHFAlgorithm::check() [with unsigned int span = 64; Abundance_t = unsigned char; NodeState_t = unsigned char]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:13:16: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:311:21: warning: unused variable 'abundance' [-Wunused-variable] + Abundance_t abundance = (*_abundanceMap)[count.value]; + ^~~~~~~~~ +[ 79%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_32.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp +[ 79%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_64.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_64.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp:6: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp:6: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of 'void gatb::core::kmer::impl::MPHFAlgorithm::check() [with unsigned int span = 96; Abundance_t = unsigned char; NodeState_t = unsigned char]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp:13:16: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:311:21: warning: unused variable 'abundance' [-Wunused-variable] + Abundance_t abundance = (*_abundanceMap)[count.value]; + ^~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp:2: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp:2: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of 'bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >; Edge = gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >; Graph = gatb::core::debruijn::impl::GraphTemplate, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, boost::variant, gatb::core::debruijn::impl::GraphData<32>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<64>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<96>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<128>, boost::mpl::l_end> > > > > > >]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:852:16: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::set, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, std::less, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > >, std::allocator, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > > >::size_type' {aka 'unsigned int'} [-Wformat=] - if (debug) printf("%lu-bubble mean %d, stdev %.1f\n",consensuses.size(),mean,stdev); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of 'bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t >; Edge = gatb::core::debruijn::impl::Edge_t > >; Graph = gatb::core::debruijn::impl::GraphTemplate >, gatb::core::debruijn::impl::Edge_t > >, boost::variant > >]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp:18:16: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::set > >, std::less > > >, std::allocator > > > >::size_type' {aka 'unsigned int'} [-Wformat=] +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:7: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + props->add (0, "host"); + ^ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_32.cpp:1: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); @@ -5103,31 +4969,44 @@ from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp:2: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -[ 78%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_64.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_64.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:31, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_32.cpp:3: +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:7: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + props->add (0, "host"); + ^ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:7: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + props->add (0, "host"); + ^ +[ 80%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_96.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:7: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] props->add (0, "host"); ^ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp:2: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of 'bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >; Edge = gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >; Graph = gatb::core::debruijn::impl::GraphTemplate, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, boost::variant, gatb::core::debruijn::impl::GraphData<32>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<64>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<96>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<128>, boost::mpl::l_end> > > > > > >]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:852:16: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::set, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, std::less, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > >, std::allocator, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > > >::size_type' {aka 'unsigned int'} [-Wformat=] - if (debug) printf("%lu-bubble mean %d, stdev %.1f\n",consensuses.size(),mean,stdev); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of 'bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t >; Edge = gatb::core::debruijn::impl::Edge_t > >; Graph = gatb::core::debruijn::impl::GraphTemplate >, gatb::core::debruijn::impl::Edge_t > >, boost::variant > >]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp:18:16: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::set > >, std::less > > >, std::allocator > > > >::size_type' {aka 'unsigned int'} [-Wformat=] In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, @@ -5135,7 +5014,70 @@ from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<96>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] + memset (_data, 0, _blockSize*sizeof(Item)); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<96>::Count' declared here + struct Count : tools::misc::Abundance + ^~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<64>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] + memset (_data, 0, _blockSize*sizeof(Item)); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<64>::Count' declared here + struct Count : tools::misc::Abundance + ^~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] + memset (_data, 0, _blockSize*sizeof(Item)); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<>::Count' declared here + struct Count : tools::misc::Abundance + ^~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = unsigned int]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here @@ -5145,22 +5087,10 @@ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<128>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp:2: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, @@ -5168,7 +5098,49 @@ from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<128>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] + memset (_data, 0, _blockSize*sizeof(Item)); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<128>::Count' declared here + struct Count : tools::misc::Abundance + ^~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<96>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] + memset (_data, 0, _blockSize*sizeof(Item)); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<96>::Count' declared here + struct Count : tools::misc::Abundance + ^~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = unsigned int]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here @@ -5178,7 +5150,7 @@ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<64>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ @@ -5189,7 +5161,7 @@ from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = unsigned int]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here @@ -5199,7 +5171,7 @@ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ @@ -5273,18 +5245,39 @@ from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<64>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] + memset (_data, 0, _blockSize*sizeof(Item)); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<64>::Count' declared here + struct Count : tools::misc::Abundance + ^~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = unsigned int]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<96>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<128>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<96>::Count' declared here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<128>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, @@ -5294,7 +5287,7 @@ from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = unsigned int]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here @@ -5304,21 +5297,54 @@ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<64>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp:2: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of 'bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >; Edge = gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >; Graph = gatb::core::debruijn::impl::GraphTemplate, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, boost::variant, gatb::core::debruijn::impl::GraphData<32>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<64>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<96>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<128>, boost::mpl::l_end> > > > > > >]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:852:16: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::set, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, std::less, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > >, std::allocator, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > > >::size_type' {aka 'unsigned int'} [-Wformat=] - if (debug) printf("%lu-bubble mean %d, stdev %.1f\n",consensuses.size(),mean,stdev); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of 'bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t >; Edge = gatb::core::debruijn::impl::Edge_t > >; Graph = gatb::core::debruijn::impl::GraphTemplate >, gatb::core::debruijn::impl::Edge_t > >, boost::variant > >]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp:18:16: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::set > >, std::less > > >, std::allocator > > > >::size_type' {aka 'unsigned int'} [-Wformat=] -[ 78%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_96.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_96.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] + memset (_data, 0, _blockSize*sizeof(Item)); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<>::Count' declared here + struct Count : tools::misc::Abundance + ^~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = unsigned int]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]' +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'struct gatb::core::kmer::impl::Kmer<96>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] + memset (_data, 0, _blockSize*sizeof(Item)); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<96>::Count' declared here + struct Count : tools::misc::Abundance + ^~~~~ +[ 80%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_128.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, @@ -5326,94 +5352,104 @@ from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_96.cpp:2: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_96.cpp:2: +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of 'bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >; Edge = gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >; Graph = gatb::core::debruijn::impl::GraphTemplate, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, boost::variant, gatb::core::debruijn::impl::GraphData<32>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<64>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<96>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<128>, boost::mpl::l_end> > > > > > >]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:852:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::set, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, std::less, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > >, std::allocator, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > > >::size_type' {aka 'unsigned int'} [-Wformat=] if (debug) printf("%lu-bubble mean %d, stdev %.1f\n",consensuses.size(),mean,stdev); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of 'bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t >; Edge = gatb::core::debruijn::impl::Edge_t > >; Graph = gatb::core::debruijn::impl::GraphTemplate >, gatb::core::debruijn::impl::Edge_t > >, boost::variant > >]': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_96.cpp:18:16: required from here -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::set > >, std::less > > >, std::allocator > > > >::size_type' {aka 'unsigned int'} [-Wformat=] -[ 79%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_128.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp -[ 79%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_32.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of 'bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t >; Edge = gatb::core::debruijn::impl::Edge_t > >; Graph = gatb::core::debruijn::impl::GraphTemplate >, gatb::core::debruijn::impl::Edge_t > >, boost::variant > >]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp:18:16: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::set > >, std::less > > >, std::allocator > > > >::size_type' {aka 'unsigned int'} [-Wformat=] +[ 80%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_32.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp +[ 81%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_64.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_64.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp:2: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of 'bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >; Edge = gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >; Graph = gatb::core::debruijn::impl::GraphTemplate, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, boost::variant, gatb::core::debruijn::impl::GraphData<32>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<64>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<96>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<128>, boost::mpl::l_end> > > > > > >]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:852:16: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::set, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, std::less, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > >, std::allocator, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > > >::size_type' {aka 'unsigned int'} [-Wformat=] + if (debug) printf("%lu-bubble mean %d, stdev %.1f\n",consensuses.size(),mean,stdev); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of 'bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t >; Edge = gatb::core::debruijn::impl::Edge_t > >; Graph = gatb::core::debruijn::impl::GraphTemplate >, gatb::core::debruijn::impl::Edge_t > >, boost::variant > >]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp:18:16: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::set > >, std::less > > >, std::allocator > > > >::size_type' {aka 'unsigned int'} [-Wformat=] In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -[ 79%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_64.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_64.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:2: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - props->add (0, "host"); - ^ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:2: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - props->add (0, "host"); - ^ -[ 79%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_64.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_64.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_64.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp:2: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of 'bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >; Edge = gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >; Graph = gatb::core::debruijn::impl::GraphTemplate, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, boost::variant, gatb::core::debruijn::impl::GraphData<32>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<64>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<96>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<128>, boost::mpl::l_end> > > > > > >]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:852:16: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::set, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, std::less, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > >, std::allocator, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > > >::size_type' {aka 'unsigned int'} [-Wformat=] + if (debug) printf("%lu-bubble mean %d, stdev %.1f\n",consensuses.size(),mean,stdev); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of 'bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t >; Edge = gatb::core::debruijn::impl::Edge_t > >; Graph = gatb::core::debruijn::impl::GraphTemplate >, gatb::core::debruijn::impl::Edge_t > >, boost::variant > >]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp:18:16: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::set > >, std::less > > >, std::allocator > > > >::size_type' {aka 'unsigned int'} [-Wformat=] +[ 81%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_96.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_96.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_96.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:2: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - props->add (0, "host"); - ^ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_96.cpp:2: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of 'bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >; Edge = gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >; Graph = gatb::core::debruijn::impl::GraphTemplate, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, boost::variant, gatb::core::debruijn::impl::GraphData<32>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<64>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<96>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<128>, boost::mpl::l_end> > > > > > >]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:852:16: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::set, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, std::less, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > >, std::allocator, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > > >::size_type' {aka 'unsigned int'} [-Wformat=] + if (debug) printf("%lu-bubble mean %d, stdev %.1f\n",consensuses.size(),mean,stdev); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of 'bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t >; Edge = gatb::core::debruijn::impl::Edge_t > >; Graph = gatb::core::debruijn::impl::GraphTemplate >, gatb::core::debruijn::impl::Edge_t > >, boost::variant > >]': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_96.cpp:18:16: required from here +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::set > >, std::less > > >, std::allocator > > > >::size_type' {aka 'unsigned int'} [-Wformat=] +[ 82%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_128.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_64.cpp:1: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -[ 80%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_96.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:31, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_64.cpp:3: +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] props->add (0, "host"); @@ -5425,7 +5461,7 @@ from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = unsigned int]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here @@ -5435,7 +5471,7 @@ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<128>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ @@ -5446,7 +5482,7 @@ from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = unsigned int]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here @@ -5456,7 +5492,7 @@ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<96>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ @@ -5467,7 +5503,7 @@ from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = unsigned int]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here @@ -5477,7 +5513,7 @@ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<64>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ @@ -5488,7 +5524,7 @@ from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = unsigned int]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here @@ -5498,10 +5534,50 @@ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ +[ 82%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_32.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:2: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + props->add (0, "host"); + ^ +[ 82%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_64.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_64.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp +[ 83%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_96.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:2: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] + props->add (0, "host"); + ^ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, @@ -5509,7 +5585,7 @@ from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = unsigned int]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here @@ -5519,7 +5595,7 @@ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<128>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ @@ -5530,7 +5606,7 @@ from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = unsigned int]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here @@ -5540,7 +5616,7 @@ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<96>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ @@ -5551,7 +5627,7 @@ from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = unsigned int]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here @@ -5561,7 +5637,7 @@ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<64>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ @@ -5572,7 +5648,7 @@ from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of 'gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = unsigned int]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from 'gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here @@ -5582,7 +5658,7 @@ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ @@ -5603,8 +5679,45 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] props->add (0, "host"); ^ -[ 81%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_96.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_96.cpp +make[4]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' +[ 83%] Built target gatbcore-static +make -f test/unit/CMakeFiles/gatb-core-cppunit.dir/build.make test/unit/CMakeFiles/gatb-core-cppunit.dir/depend +make[4]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/test/unit /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/test/unit/CMakeFiles/gatb-core-cppunit.dir/DependInfo.cmake --color= +Scanning dependencies of target gatb-core-cppunit +make[4]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' +make -f test/unit/CMakeFiles/gatb-core-cppunit.dir/build.make test/unit/CMakeFiles/gatb-core-cppunit.dir/build +make[4]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' +[ 83%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/bank/TestBank.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/bank/TestBank.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp +[ 83%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_128.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_128.cpp +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp: In member function 'void gatb::tests::TestBank::bank_checkSample1_aux(const string&, gatb::core::bank::impl::BankFasta::Iterator::CommentMode_e)': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp:118:47: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] + snprintf (buffer, sizeof(buffer), "seq%ld%s", i+1, (mode == BankFasta::Iterator::FULL ? " generic" : "")); + ^~~~~~~~~~ ~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp: In member function 'void gatb::tests::TestBank::bank_checkSample2_aux(const string&)': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp:187:47: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] + snprintf (buffer, sizeof(buffer), "seq%ld", nbSeq+1); + ^~~~~~~~ ~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp: In member function 'void gatb::tests::TestBank::bank_perf1()': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp:678:17: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'u_int64_t' {aka 'long long unsigned int'} [-Wformat=] + printf ("size=%ld time=%ld => rate=%.3f MB/s \n", + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + totalSize, t1-t0, + ~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp:678:17: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'gatb::core::system::ITime::Value' {aka 'long long unsigned int'} [-Wformat=] +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_128.cpp:1: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, @@ -5689,19 +5802,8 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_96.cpp:1: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:31, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_96.cpp:3: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_128.cpp:3: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] props->add (0, "host"); @@ -5790,35 +5892,25 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ -[ 81%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_128.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_128.cpp.o -c 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CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_32.cpp -[ 82%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_64.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function 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-Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_96.cpp -[ 82%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_128.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_128.cpp +[ 84%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/bank/TestLeon.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/bank/TestLeon.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/bank/TestLeon.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_128.cpp:1: + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/bank/TestLeon.cpp:32: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:31, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_128.cpp:3: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] - props->add (0, "host"); - ^ -[ 83%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_32.cpp.o +[ 84%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/bank/TestSequence.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/bank/TestSequence.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/bank/TestSequence.cpp +[ 85%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_32.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_32.cpp +[ 86%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/bcalm/TestBcalm.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/bcalm/TestBcalm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/bcalm/TestBcalm.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, @@ -5830,24 +5922,36 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -[ 83%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_64.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_64.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_64.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:31, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_32.cpp:3: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function 'static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] props->add (0, "host"); ^ -[ 83%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_96.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_96.cpp -[ 84%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_128.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_128.cpp -[ 84%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_32.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_32.cpp -[ 85%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_64.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_64.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_64.cpp -[ 85%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_96.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_96.cpp +[ 86%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestDebruijn.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestDebruijn.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp:33: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +[ 86%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestDebruijnUnitigs.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestDebruijnUnitigs.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijnUnitigs.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijnUnitigs.cpp:33: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +[ 86%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_64.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_64.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_64.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, @@ -5865,6 +5969,8 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] props->add (0, "host"); ^ +[ 86%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_96.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_96.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, @@ -5882,84 +5988,8 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to 'va_list' {aka 'char*'} [-Wwrite-strings] 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-I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestSimplificationsUnitigs.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/debruijn/TestSimplificationsUnitigs.cpp -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestDebloom.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/kmer/TestDebloom.cpp -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestKmer.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/kmer/TestKmer.cpp -[ 92%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestDSK.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestDSK.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/kmer/TestDSK.cpp -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp: In member function 'void gatb::tests::TestBank::bank_checkSample1_aux(const string&, gatb::core::bank::impl::BankFasta::Iterator::CommentMode_e)': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp:118:47: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] - snprintf (buffer, sizeof(buffer), "seq%ld%s", i+1, (mode == BankFasta::Iterator::FULL ? " generic" : "")); - ^~~~~~~~~~ ~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp: In member function 'void gatb::tests::TestBank::bank_checkSample2_aux(const string&)': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp:187:47: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] - snprintf (buffer, sizeof(buffer), "seq%ld", nbSeq+1); - ^~~~~~~~ ~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp: In member function 'void gatb::tests::TestBank::bank_perf1()': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp:678:17: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'u_int64_t' {aka 'long long unsigned int'} [-Wformat=] - printf ("size=%ld time=%ld => rate=%.3f MB/s \n", - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - totalSize, t1-t0, - ~~~~~~~~~ -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp:678:17: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'gatb::core::system::ITime::Value' {aka 'long long unsigned int'} [-Wformat=] In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, @@ -5969,6 +5999,23 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +[ 88%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_128.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_128.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_128.cpp +[ 88%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_32.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_32.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_32.cpp +[ 89%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_64.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall 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-msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_96.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_96.cpp +make -f tools/CMakeFiles/dbginfo.dir/build.make tools/CMakeFiles/dbginfo.dir/depend +make[4]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/tools /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/tools /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/tools/CMakeFiles/dbginfo.dir/DependInfo.cmake --color= +Scanning dependencies of target dbginfo +make[4]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' +make -f tools/CMakeFiles/dbginfo.dir/build.make tools/CMakeFiles/dbginfo.dir/build +make[4]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' +[ 90%] Building CXX object tools/CMakeFiles/dbginfo.dir/dbginfo.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/tools && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/dbginfo.dir/dbginfo.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/tools/dbginfo.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, @@ -5979,25 +6026,20 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijnUnitigs.cpp:33: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/tools/leon.cpp:20: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +make -f tools/CMakeFiles/dbgh5.dir/build.make tools/CMakeFiles/dbgh5.dir/depend +make[4]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/tools /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/tools /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/tools/CMakeFiles/dbgh5.dir/DependInfo.cmake --color= +Scanning dependencies of target dbgh5 +make[4]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' +make -f tools/CMakeFiles/dbgh5.dir/build.make tools/CMakeFiles/dbgh5.dir/build +make[4]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' +[ 91%] Building CXX object tools/CMakeFiles/dbgh5.dir/dbgh5.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/tools && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/dbgh5.dir/dbgh5.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/tools/dbgh5.cpp +[ 91%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestSimplificationsUnitigs.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestSimplificationsUnitigs.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/debruijn/TestSimplificationsUnitigs.cpp +[ 91%] Linking CXX executable ../bin/None/dbginfo +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/dbginfo.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/dbginfo.dir/dbginfo.cpp.o -o ../bin/None/dbginfo -Wl,-rpath,/usr/lib/i386-linux-gnu/hdf5/serial: ../lib/None/libgatbcore.a -ldl -lpthread -lz /usr/lib/i386-linux-gnu/hdf5/serial/libhdf5.so -lpthread -lsz -lz -ldl -lm In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, @@ -6008,6 +6050,10 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/tools/dbgh5.cpp: In function 'void sendEmail(gatb::core::tools::misc::IProperties*, gatb::core::tools::misc::IProperties*)': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/tools/dbgh5.cpp:127:13: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] + ::system (cmd.str().c_str()); + ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, @@ -6018,26 +6064,13 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/bank/TestLeon.cpp:32: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp:33: -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - printf("rank array : size %lu \n",_ranks.size()); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +[ 92%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestDSK.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestDSK.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/kmer/TestDSK.cpp +[ 92%] Linking CXX executable ../bin/None/dbgh5 +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/dbgh5.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/dbgh5.dir/dbgh5.cpp.o -o ../bin/None/dbgh5 -Wl,-rpath,/usr/lib/i386-linux-gnu/hdf5/serial: ../lib/None/libgatbcore.a -ldl -lpthread -lz /usr/lib/i386-linux-gnu/hdf5/serial/libhdf5.so -lpthread -lsz -lz -ldl -lm +[ 92%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestDebloom.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestDebloom.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/kmer/TestDebloom.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, @@ -6057,20 +6090,34 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ -[ 93%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestKmerBank.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestKmerBank.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/kmer/TestKmerBank.cpp -[ 93%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestMPHF.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestMPHF.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/kmer/TestMPHF.cpp -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/tools/dbgh5.cpp: In function 'void sendEmail(gatb::core::tools::misc::IProperties*, gatb::core::tools::misc::IProperties*)': -/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/tools/dbgh5.cpp:127:13: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] - ::system (cmd.str().c_str()); - ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -[ 94%] Linking CXX executable ../bin/None/leon +[ 92%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestKmer.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestKmer.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/kmer/TestKmer.cpp +make -f tools/CMakeFiles/leon.dir/build.make tools/CMakeFiles/leon.dir/depend +make[4]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/tools /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/tools /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/tools/CMakeFiles/leon.dir/DependInfo.cmake --color= +Scanning dependencies of target leon +make[4]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' +make -f tools/CMakeFiles/leon.dir/build.make tools/CMakeFiles/leon.dir/build +make[4]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' +[ 92%] Building CXX object tools/CMakeFiles/leon.dir/leon.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/tools && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/leon.dir/leon.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/tools/leon.cpp +In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, + from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/tools/leon.cpp:20: +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': +/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + printf("rank array : size %lu \n",_ranks.size()); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +[ 93%] Linking CXX executable ../bin/None/leon cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/leon.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/leon.dir/leon.cpp.o -o ../bin/None/leon -Wl,-rpath,/usr/lib/i386-linux-gnu/hdf5/serial: ../lib/None/libgatbcore.a -ldl -lpthread -lz /usr/lib/i386-linux-gnu/hdf5/serial/libhdf5.so -lpthread -lsz -lz -ldl -lm -[ 94%] Linking CXX executable ../bin/None/dbginfo -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/dbginfo.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/dbginfo.dir/dbginfo.cpp.o -o ../bin/None/dbginfo -Wl,-rpath,/usr/lib/i386-linux-gnu/hdf5/serial: ../lib/None/libgatbcore.a -ldl -lpthread -lz /usr/lib/i386-linux-gnu/hdf5/serial/libhdf5.so 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CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestMPHF.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/kmer/TestMPHF.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, @@ -6079,37 +6126,30 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -[ 94%] Linking CXX executable ../bin/None/dbgh5 -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/tools && 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-I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/tools/math/TestMath.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/tools/math/TestMath.cpp -[ 98%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/misc/TestMisc.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/tools/misc/TestMisc.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/tools/misc/TestMisc.cpp -[100%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/storage/TestStorage.cpp.o -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/tools/storage/TestStorage.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/tools/storage/TestStorage.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/tools/collections/TestMap.cpp:24: @@ -6117,6 +6157,10 @@ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +[ 98%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/misc/TestMisc.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/tools/misc/TestMisc.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/tools/misc/TestMisc.cpp +[100%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/storage/TestStorage.cpp.o +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/tools/storage/TestStorage.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/tools/storage/TestStorage.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, @@ -6158,7 +6202,7 @@ dh_testroot -O--sourcedirectory=gatb-core dh_prep -O--sourcedirectory=gatb-core dh_auto_install -O--sourcedirectory=gatb-core - cd obj-i686-linux-gnu && make -j18 install DESTDIR=/build/gatb-core-1.4.1\+git20181225.44d5a44\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-i686-linux-gnu && make -j10 install DESTDIR=/build/gatb-core-1.4.1\+git20181225.44d5a44\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core -B/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/CMakeFiles /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/CMakeFiles/progress.marks @@ -6173,19 +6217,19 @@ make -f thirdparty/CMakeFiles/thirdparty_copy.dir/build.make thirdparty/CMakeFiles/thirdparty_copy.dir/build make[3]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/thirdparty && /usr/bin/cmake -E make_directory /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/json +make[3]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/CMakeFiles/gatbcore-static.dir/DependInfo.cmake --color= cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/thirdparty && /usr/bin/cmake -E make_directory /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF +make[3]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/CMakeFiles/gatbcore-dynamic.dir/DependInfo.cmake --color= cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/thirdparty && /usr/bin/cmake -E copy_if_different /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty/BooPHF/BooPHF.h /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/BooPHF/ cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/thirdparty && /usr/bin/cmake -E copy_if_different /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty/json/json.hpp /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/include/None/json/ make[3]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/CMakeFiles/gatbcore-dynamic.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/src/CMakeFiles/gatbcore-static.dir/DependInfo.cmake --color= [ 0%] Built target thirdparty_copy make[3]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' -make -f src/CMakeFiles/gatbcore-dynamic.dir/build.make src/CMakeFiles/gatbcore-dynamic.dir/build -make[3]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' make -f src/CMakeFiles/gatbcore-static.dir/build.make src/CMakeFiles/gatbcore-static.dir/build +make[3]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' +make -f src/CMakeFiles/gatbcore-dynamic.dir/build.make src/CMakeFiles/gatbcore-dynamic.dir/build make[3]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'src/CMakeFiles/gatbcore-static.dir/build'. make[3]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' @@ -6197,7 +6241,6 @@ make -f tools/CMakeFiles/dbginfo.dir/build.make tools/CMakeFiles/dbginfo.dir/depend make -f tools/CMakeFiles/dbgh5.dir/build.make tools/CMakeFiles/dbgh5.dir/depend make -f tools/CMakeFiles/leon.dir/build.make tools/CMakeFiles/leon.dir/depend -[ 86%] Built target gatbcore-dynamic make[3]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/tools /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/tools /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/tools/CMakeFiles/dbginfo.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' @@ -6206,29 +6249,30 @@ cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/tools /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/tools /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/tools/CMakeFiles/leon.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/test/unit /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/test/unit/CMakeFiles/gatb-core-cppunit.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' -make -f tools/CMakeFiles/dbginfo.dir/build.make tools/CMakeFiles/dbginfo.dir/build +[ 86%] Built target gatbcore-dynamic make[3]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' make -f tools/CMakeFiles/dbgh5.dir/build.make tools/CMakeFiles/dbgh5.dir/build make[3]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' +make -f tools/CMakeFiles/dbginfo.dir/build.make tools/CMakeFiles/dbginfo.dir/build +make[3]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' make -f tools/CMakeFiles/leon.dir/build.make tools/CMakeFiles/leon.dir/build make[3]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' make -f test/unit/CMakeFiles/gatb-core-cppunit.dir/build.make test/unit/CMakeFiles/gatb-core-cppunit.dir/build make[3]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tools/CMakeFiles/dbgh5.dir/build'. +make[3]: Nothing to be done for 'tools/CMakeFiles/dbginfo.dir/build'. make[3]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'tools/CMakeFiles/leon.dir/build'. make[3]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tools/CMakeFiles/dbginfo.dir/build'. +make[3]: Nothing to be done for 'tools/CMakeFiles/dbgh5.dir/build'. make[3]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' -[ 87%] Built target dbgh5 -[ 88%] Built target dbginfo make[3]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'test/unit/CMakeFiles/gatb-core-cppunit.dir/build'. make[3]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' -[ 89%] Built target leon +[ 87%] Built target dbginfo +[ 88%] Built target leon +[ 89%] Built target dbgh5 [100%] Built target gatb-core-cppunit make[2]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-i686-linux-gnu/CMakeFiles 0 @@ -6240,342 +6284,342 @@ /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: 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/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl/Cell.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl/CollectionFile.hpp --- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl/StorageFile.hpp --- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl/CollectionHDF5Patch.hpp --- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl/StorageTools.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl/Storage.tpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl/CollectionHDF5.hpp --- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl/Storage.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl/StorageTools.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl/StorageHDF5.hpp --- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl/Cell.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl/StorageFile.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl/CollectionHDF5Patch.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl/Storage.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/storage/api -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/storage/api/ICell.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/collections +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/BagPartition.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/BooPHF.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/Bloom.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/BagFile.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/CollectionCache.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/ContainerSet.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/IteratorFile.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/MapMPHF.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/BagCache.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/Hash16.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/IterableHelpers.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/OAHash.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/CollectionAbstract.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/BloomGroup.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/collections/api +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/collections/api/Container.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/collections/api/Iterable.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/collections/api/Collection.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/collections/api/Bag.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/compression --- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/compression/Leon.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/compression/DnaCoder.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/compression/CompressionUtils.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/compression/HeaderCoder.hpp --- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/compression/DnaCoder.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/compression/Leon.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/compression/RangeCoder.hpp --- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/tools/designpattern --- Installing: 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-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl --- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/CountProcessorProxy.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/BloomBuilder.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/PartitionsCommand.hpp --- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/CountProcessorSolidity.hpp --- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/BankKmers.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/DebloomAlgorithm.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/RepartitionAlgorithm.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/Configuration.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/CountProcessor.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/Sequence2SuperKmer.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/PartiInfo.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/Model.hpp --- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/BankKmerIterator.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/BankKmers.hpp +-- Installing: 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/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/CountProcessorDump.hpp --- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/CountProcessorAbstract.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/CountProcessorHistogram.hpp --- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/CountProcessor.hpp --- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/DebloomAlgorithm.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/CountProcessorProxy.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/LinearCounter.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/Model.pri +-- Installing: 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Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/api --- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/api/ICountProcessor.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/api/IModel.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/api/ICountProcessor.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/impl +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/impl/System.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/impl/ThreadLinux.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/impl/MemoryCommon.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/impl/FileSystemLinux.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/impl/TimeCommon.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/impl/FileSystemCommon.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/impl/FileSystemMacos.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/impl/SystemInfoCommon.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/impl/ThreadMacos.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/api +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/api/Exception.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/api/ISystemInfo.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/api/ITime.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/api/ISmartPointer.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/api/types.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/api/IMemory.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/api/IFileSystem.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/api/IThread.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/api/config_sha1.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/impl +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/BranchingAlgorithm.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/GraphUnitigs.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/Graph.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/LinkTigs.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/UnitigsConstructionAlgorithm.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/Frontline.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/dag_vector.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/ContainerNode.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/NodesDeleter.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/ExtremityInfo.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/Traversal.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/rank_vector.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/Terminator.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/Simplifications.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/IterativeExtensions.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/api +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/api/IContainerNode.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bcalm2 +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bcalm2/unionFind.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bcalm2/ThreadPool.h +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bcalm2/binSeq.h +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bcalm2/ograph.h +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bcalm2/bglue_algo.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bcalm2/ographBin.h +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bcalm2/logging.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bcalm2/bcalm_algo.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/gatb_core.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/impl +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/impl/BankAlbum.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/impl/Alphabet.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/impl/BankRandom.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/impl/Banks.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/impl/BankHelpers.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/impl/BankSplitter.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/impl/BankConverterAlgorithm.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/impl/BankBinary.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/impl/AbstractBank.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/impl/BankComposite.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/impl/Bank.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/impl/BankFasta.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/impl/BankStrings.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/api +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/api/Sequence.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/api/IBank.hpp +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/api/IAlphabet.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/api/config.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test/gatb-core-cppunit -- Set runtime path of "/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test/gatb-core-cppunit" to "" -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db --- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/sample1.fa --- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/sample.fastq.gz --- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/leon1.fastq --- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/reads1.fa.gz --- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/reads1.fa --- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/leon2.fastq.leon-ref --- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/sample1.fa.gz --- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/query.fa.gz --- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/celegans_reads.h5 --- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/query.fa --- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/reads3.fa.gz --- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/sample.fastq +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/leon1.fastq.leon-ref -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/album.txt -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/reads1_list_ids.txt --- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/microsnp.fa +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/sample.fastq -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/README.md +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/leon1.fastq +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/sample.fastq.gz +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/query.fa +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/celegans_reads.h5 +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/query.fa.gz +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/reads2.fa -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/sample2.fa +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/reads1.fa.gz +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/sample1.fa.gz +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/reads1.fa -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/leon2.fastq --- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/reads2.fa --- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/leon1.fastq.leon-ref +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/sample1.fa +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/microsnp.fa +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/leon2.fastq.leon-ref +-- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/reads3.fa.gz -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/bin/dbgh5 -- Set runtime path of "/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/bin/dbgh5" to "" -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/bin/dbginfo @@ -6632,43 +6676,45 @@ dh_strip -O--sourcedirectory=gatb-core dh_makeshlibs -O--sourcedirectory=gatb-core dh_shlibdeps -O--sourcedirectory=gatb-core +dpkg-shlibdeps: warning: symbol H5Tclose used by debian/libgatbcore2/usr/lib/i386-linux-gnu/libgatbcore.so.2 found in none of the libraries +dpkg-shlibdeps: warning: symbol H5Dset_extent used by debian/libgatbcore2/usr/lib/i386-linux-gnu/libgatbcore.so.2 found in none of the libraries +dpkg-shlibdeps: warning: symbol pthread_create used by debian/libgatbcore2/usr/lib/i386-linux-gnu/libgatbcore.so.2 found in none of the libraries +dpkg-shlibdeps: warning: symbol gzread used by debian/libgatbcore2/usr/lib/i386-linux-gnu/libgatbcore.so.2 found in none of the libraries +dpkg-shlibdeps: warning: symbol gzopen used by debian/libgatbcore2/usr/lib/i386-linux-gnu/libgatbcore.so.2 found in none of the libraries +dpkg-shlibdeps: warning: symbol H5Gopen2 used by debian/libgatbcore2/usr/lib/i386-linux-gnu/libgatbcore.so.2 found in none of the libraries +dpkg-shlibdeps: warning: symbol H5Gclose used by debian/libgatbcore2/usr/lib/i386-linux-gnu/libgatbcore.so.2 found in none of the libraries +dpkg-shlibdeps: warning: symbol H5Gcreate2 used by debian/libgatbcore2/usr/lib/i386-linux-gnu/libgatbcore.so.2 found in none of the libraries dpkg-shlibdeps: warning: symbol gzseek used by debian/libgatbcore2/usr/lib/i386-linux-gnu/libgatbcore.so.2 found in none of the libraries -dpkg-shlibdeps: warning: symbol H5Fcreate used by debian/libgatbcore2/usr/lib/i386-linux-gnu/libgatbcore.so.2 found in none of the libraries -dpkg-shlibdeps: warning: symbol H5Tcopy used by debian/libgatbcore2/usr/lib/i386-linux-gnu/libgatbcore.so.2 found in none of the libraries -dpkg-shlibdeps: warning: symbol pthread_join used by debian/libgatbcore2/usr/lib/i386-linux-gnu/libgatbcore.so.2 found in none of the libraries -dpkg-shlibdeps: warning: symbol H5T_NATIVE_UINT16_g used by debian/libgatbcore2/usr/lib/i386-linux-gnu/libgatbcore.so.2 found in none of the libraries -dpkg-shlibdeps: warning: symbol H5Pcreate used by debian/libgatbcore2/usr/lib/i386-linux-gnu/libgatbcore.so.2 found in none of the libraries -dpkg-shlibdeps: warning: symbol H5Adelete used by debian/libgatbcore2/usr/lib/i386-linux-gnu/libgatbcore.so.2 found in none of the libraries -dpkg-shlibdeps: warning: symbol H5P_CLS_DATASET_CREATE_ID_g used by debian/libgatbcore2/usr/lib/i386-linux-gnu/libgatbcore.so.2 found in none of the libraries -dpkg-shlibdeps: warning: symbol H5Sselect_hyperslab used by debian/libgatbcore2/usr/lib/i386-linux-gnu/libgatbcore.so.2 found in none of the libraries -dpkg-shlibdeps: warning: symbol gzwrite used by debian/libgatbcore2/usr/lib/i386-linux-gnu/libgatbcore.so.2 found in none of the libraries +dpkg-shlibdeps: warning: symbol H5Dvlen_reclaim used by debian/libgatbcore2/usr/lib/i386-linux-gnu/libgatbcore.so.2 found in none of the libraries dpkg-shlibdeps: warning: 57 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/gatb-core/usr/bin/dbgh5 debian/gatb-core/usr/bin/leon debian/gatb-core/usr/lib/gatb-core/gatb-core-cppunit debian/gatb-core/usr/bin/dbginfo were not linked against libsz.so.2 (they use none of the library's symbols) -dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/gatb-core/usr/bin/dbgh5 debian/gatb-core/usr/bin/leon debian/gatb-core/usr/lib/gatb-core/gatb-core-cppunit debian/gatb-core/usr/bin/dbginfo were not linked against libdl.so.2 (they use none of the library's symbols) +dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/gatb-core/usr/bin/leon debian/gatb-core/usr/lib/gatb-core/gatb-core-cppunit debian/gatb-core/usr/bin/dbginfo debian/gatb-core/usr/bin/dbgh5 were not linked against libdl.so.2 (they use none of the library's symbols) +dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/gatb-core/usr/bin/leon debian/gatb-core/usr/lib/gatb-core/gatb-core-cppunit debian/gatb-core/usr/bin/dbginfo debian/gatb-core/usr/bin/dbgh5 were not linked against libsz.so.2 (they use none of the library's symbols) dh_installdeb -O--sourcedirectory=gatb-core dh_gencontrol -O--sourcedirectory=gatb-core dpkg-gencontrol: warning: Depends field of package libgatbcore-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package gatb-core-testdata: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums -O--sourcedirectory=gatb-core dh_builddeb -O--sourcedirectory=gatb-core -dpkg-deb: building package 'gatb-core' in '../gatb-core_1.4.1+git20181225.44d5a44+dfsg-3_i386.deb'. -dpkg-deb: building package 'gatb-core-dbgsym' in '../gatb-core-dbgsym_1.4.1+git20181225.44d5a44+dfsg-3_i386.deb'. dpkg-deb: building package 'libgatbcore2' in '../libgatbcore2_1.4.1+git20181225.44d5a44+dfsg-3_i386.deb'. -dpkg-deb: building package 'libgatbcore2-dbgsym' in '../libgatbcore2-dbgsym_1.4.1+git20181225.44d5a44+dfsg-3_i386.deb'. dpkg-deb: building package 'libgatbcore-dev' in '../libgatbcore-dev_1.4.1+git20181225.44d5a44+dfsg-3_i386.deb'. +dpkg-deb: building package 'gatb-core-dbgsym' in '../gatb-core-dbgsym_1.4.1+git20181225.44d5a44+dfsg-3_i386.deb'. +dpkg-deb: building package 'gatb-core' in '../gatb-core_1.4.1+git20181225.44d5a44+dfsg-3_i386.deb'. dpkg-deb: building package 'gatb-core-testdata' in '../gatb-core-testdata_1.4.1+git20181225.44d5a44+dfsg-3_all.deb'. +dpkg-deb: building package 'libgatbcore2-dbgsym' in '../libgatbcore2-dbgsym_1.4.1+git20181225.44d5a44+dfsg-3_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../gatb-core_1.4.1+git20181225.44d5a44+dfsg-3_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/18873/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/18873/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/31135 and its subdirectories -I: Current time: Wed Jul 29 04:47:58 -12 2020 -I: pbuilder-time-stamp: 1596041278 +I: removing directory /srv/workspace/pbuilder/18873 and its subdirectories +I: Current time: Fri Jun 28 01:13:23 +14 2019 +I: pbuilder-time-stamp: 1561634003