Diff of the two buildlogs: -- --- b1/build.log 2019-06-22 17:49:56.878013911 +0000 +++ b2/build.log 2019-06-22 18:01:53.564582863 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Jul 24 12:12:18 -12 2020 -I: pbuilder-time-stamp: 1595635938 +I: Current time: Sun Jun 23 07:49:59 +14 2019 +I: pbuilder-time-stamp: 1561225799 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 Wed Oct 24 07:30:12 2018 -12 +gpgv: Signature made Thu Oct 25 09:30:12 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -30,6 +30,18 @@ dpkg-source: info: applying hardening.patch I: using fakeroot in build. I: Installing the build-deps +I: user script /srv/workspace/pbuilder/6325/tmp/hooks/D01_modify_environment starting +disorder-fs debug: Running on profitbricks-build2-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/6325/tmp/hooks/D01_modify_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -136,7 +148,7 @@ Get: 67 http://cdn-fastly.deb.debian.org/debian buster/main i386 openmpi-common all 3.1.3-11 [165 kB] Get: 68 http://cdn-fastly.deb.debian.org/debian buster/main i386 openmpi-bin i386 3.1.3-11 [200 kB] Get: 69 http://cdn-fastly.deb.debian.org/debian buster/main i386 libopenmpi-dev i386 3.1.3-11 [963 kB] -Fetched 30.4 MB in 10s (2932 kB/s) +Fetched 30.4 MB in 24s (1273 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.) @@ -437,9 +449,41 @@ 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 (95.7 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 ... 23187 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/zalign-0.9.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/zalign-0.9.1/ && 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 zalign dpkg-buildpackage: info: source version 0.9.1-4 dpkg-buildpackage: info: source distribution unstable @@ -474,7 +518,7 @@ configure: WARNING: unrecognized options: --disable-maintainer-mode checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes -checking for a thread-safe mkdir -p... /bin/mkdir -p +checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes @@ -494,10 +538,10 @@ checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none -checking for a sed that does not truncate output... /bin/sed -checking for grep that handles long lines and -e... /bin/grep -checking for egrep... /bin/grep -E -checking for fgrep... /bin/grep -F +checking for a sed that does not truncate output... /usr/bin/sed +checking for grep that handles long lines and -e... /usr/bin/grep +checking for egrep... /usr/bin/grep -E +checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B @@ -517,8 +561,8 @@ checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no -checking for a working dd... /bin/dd -checking how to truncate binary pipes... /bin/dd bs=4096 count=1 +checking for a working dd... /usr/bin/dd +checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E @@ -589,7 +633,7 @@ config.status: executing libtool commands configure: WARNING: unrecognized options: --disable-maintainer-mode dh_auto_build - make -j18 + make -j10 make[1]: Entering directory '/build/zalign-0.9.1' make all-recursive make[2]: Entering directory '/build/zalign-0.9.1' @@ -605,17 +649,10 @@ mpic++ -DHAVE_CONFIG_H -I. -I.. -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O0 -ansi -pedantic -Wall -Wextra -Wno-long-long -Wno-unused-parameter -DHAVE_MPI_CPP -lm -g -O2 -ffile-prefix-map=/build/zalign-0.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/lib/openmpi/include -c -o fastareader.o fastareader.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O0 -ansi -pedantic -Wall -Wextra -Wno-long-long -Wno-unused-parameter -DHAVE_MPI_CPP -lm -g -O2 -ffile-prefix-map=/build/zalign-0.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/lib/openmpi/include -c -o linearfickettaligner.o linearfickettaligner.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O0 -ansi -pedantic -Wall -Wextra -Wno-long-long -Wno-unused-parameter -DHAVE_MPI_CPP -lm -g -O2 -ffile-prefix-map=/build/zalign-0.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/lib/openmpi/include -c -o mpialign.o mpialign.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O0 -ansi -pedantic -Wall -Wextra -Wno-long-long -Wno-unused-parameter -DHAVE_MPI_CPP -lm -g -O2 -ffile-prefix-map=/build/zalign-0.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/lib/openmpi/include -c -o mpialignmaster.o mpialignmaster.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O0 -ansi -pedantic -Wall -Wextra -Wno-long-long -Wno-unused-parameter -DHAVE_MPI_CPP -lm -g -O2 -ffile-prefix-map=/build/zalign-0.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/lib/openmpi/include -c -o mpialignslave.o mpialignslave.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O0 -ansi -pedantic -Wall -Wextra -Wno-long-long -Wno-unused-parameter -DHAVE_MPI_CPP -lm -g -O2 -ffile-prefix-map=/build/zalign-0.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/lib/openmpi/include -c -o opt.o opt.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O0 -ansi -pedantic -Wall -Wextra -Wno-long-long -Wno-unused-parameter -DHAVE_MPI_CPP -lm -g -O2 -ffile-prefix-map=/build/zalign-0.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/lib/openmpi/include -c -o score.o score.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O0 -ansi -pedantic -Wall -Wextra -Wno-long-long -Wno-unused-parameter -DHAVE_MPI_CPP -lm -g -O2 -ffile-prefix-map=/build/zalign-0.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/lib/openmpi/include -c -o sequence.o sequence.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O0 -ansi -pedantic -Wall -Wextra -Wno-long-long -Wno-unused-parameter -DHAVE_MPI_CPP -lm -g -O2 -ffile-prefix-map=/build/zalign-0.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/lib/openmpi/include -c -o limitsplotter.o limitsplotter.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O0 -ansi -pedantic -Wall -Wextra -Wno-long-long -Wno-unused-parameter -DHAVE_MPI_CPP -lm -g -O2 -ffile-prefix-map=/build/zalign-0.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/lib/openmpi/include -c -o zalign.o zalign.cpp In file included from /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:277, from /usr/lib/i386-linux-gnu/openmpi/include/mpi.h:2684, - from ../include/blkseq.h:23, - from blkseq.cpp:20: + from ../include/alignbounds.h:23, + from alignbounds.cpp:20: /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h: In member function 'virtual void MPI::Op::Init(void (*)(const void*, void*, int, const MPI::Datatype&), bool)': /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h:121:46: warning: cast between incompatible function types from 'void (*)(void*, void*, int*, ompi_datatype_t**, void (*)(void*, void*, int*, ompi_datatype_t**))' to 'void (*)(void*, void*, int*, ompi_datatype_t**)' [-Wcast-function-type] (void)MPI_Op_create((MPI_User_function*) ompi_mpi_cxx_op_intercept, @@ -637,7 +674,8 @@ ^~~~ In file included from /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:277, from /usr/lib/i386-linux-gnu/openmpi/include/mpi.h:2684, - from mpialign.cpp:27: + from ../include/blkseq.h:23, + from blkseq.cpp:20: /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h: In member function 'virtual void MPI::Op::Init(void (*)(const void*, void*, int, const MPI::Datatype&), bool)': /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h:121:46: warning: cast between incompatible function types from 'void (*)(void*, void*, int*, ompi_datatype_t**, void (*)(void*, void*, int*, ompi_datatype_t**))' to 'void (*)(void*, void*, int*, ompi_datatype_t**)' [-Wcast-function-type] (void)MPI_Op_create((MPI_User_function*) ompi_mpi_cxx_op_intercept, @@ -647,8 +685,8 @@ ^~~~ In file included from /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:277, from /usr/lib/i386-linux-gnu/openmpi/include/mpi.h:2684, - from ../include/alignbounds.h:23, - from alignbounds.cpp:20: + from ../include/alignment.h:23, + from alignment.cpp:20: /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h: In member function 'virtual void MPI::Op::Init(void (*)(const void*, void*, int, const MPI::Datatype&), bool)': /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h:121:46: warning: cast between incompatible function types from 'void (*)(void*, void*, int*, ompi_datatype_t**, void (*)(void*, void*, int*, ompi_datatype_t**))' to 'void (*)(void*, void*, int*, ompi_datatype_t**)' [-Wcast-function-type] (void)MPI_Op_create((MPI_User_function*) ompi_mpi_cxx_op_intercept, @@ -670,7 +708,9 @@ ^~~~ In file included from /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:277, from /usr/lib/i386-linux-gnu/openmpi/include/mpi.h:2684, - from mpialignmaster.cpp:22: + from ../include/alignment.h:23, + from ../include/linearfickettaligner.h:27, + from linearfickettaligner.cpp:25: /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h: In member function 'virtual void MPI::Op::Init(void (*)(const void*, void*, int, const MPI::Datatype&), bool)': /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h:121:46: warning: cast between incompatible function types from 'void (*)(void*, void*, int*, ompi_datatype_t**, void (*)(void*, void*, int*, ompi_datatype_t**))' to 'void (*)(void*, void*, int*, ompi_datatype_t**)' [-Wcast-function-type] (void)MPI_Op_create((MPI_User_function*) ompi_mpi_cxx_op_intercept, @@ -680,8 +720,7 @@ ^~~~ In file included from /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:277, from /usr/lib/i386-linux-gnu/openmpi/include/mpi.h:2684, - from ../include/alignment.h:23, - from alignment.cpp:20: + from mpialign.cpp:27: /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h: In member function 'virtual void MPI::Op::Init(void (*)(const void*, void*, int, const MPI::Datatype&), bool)': /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h:121:46: warning: cast between incompatible function types from 'void (*)(void*, void*, int*, ompi_datatype_t**, void (*)(void*, void*, int*, ompi_datatype_t**))' to 'void (*)(void*, void*, int*, ompi_datatype_t**)' [-Wcast-function-type] (void)MPI_Op_create((MPI_User_function*) ompi_mpi_cxx_op_intercept, @@ -691,9 +730,9 @@ ^~~~ In file included from /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:277, from /usr/lib/i386-linux-gnu/openmpi/include/mpi.h:2684, - from ../include/alignment.h:23, - from ../include/linearfickettaligner.h:27, - from linearfickettaligner.cpp:25: + from ../include/blkseq.h:23, + from ../include/blkalign.h:26, + from blkalign.cpp:20: /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h: In member function 'virtual void MPI::Op::Init(void (*)(const void*, void*, int, const MPI::Datatype&), bool)': /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h:121:46: warning: cast between incompatible function types from 'void (*)(void*, void*, int*, ompi_datatype_t**, void (*)(void*, void*, int*, ompi_datatype_t**))' to 'void (*)(void*, void*, int*, ompi_datatype_t**)' [-Wcast-function-type] (void)MPI_Op_create((MPI_User_function*) ompi_mpi_cxx_op_intercept, @@ -704,7 +743,8 @@ In file included from /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:277, from /usr/lib/i386-linux-gnu/openmpi/include/mpi.h:2684, from ../include/opt.h:23, - from opt.cpp:20: + from ../include/fastareader.h:26, + from fastareader.cpp:20: /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h: In member function 'virtual void MPI::Op::Init(void (*)(const void*, void*, int, const MPI::Datatype&), bool)': /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h:121:46: warning: cast between incompatible function types from 'void (*)(void*, void*, int*, ompi_datatype_t**, void (*)(void*, void*, int*, ompi_datatype_t**))' to 'void (*)(void*, void*, int*, ompi_datatype_t**)' [-Wcast-function-type] (void)MPI_Op_create((MPI_User_function*) ompi_mpi_cxx_op_intercept, @@ -712,6 +752,29 @@ /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h:123:59: warning: cast between incompatible function types from 'void (*)(const void*, void*, int, const MPI::Datatype&)' to 'void (*)(void*, void*, int*, ompi_datatype_t**)' [-Wcast-function-type] ompi_op_set_cxx_callback(mpi_op, (MPI_User_function*) func); ^~~~ +linearfickettaligner.cpp: In member function 'void LinearFickettAligner::initializeFickettTable()': +linearfickettaligner.cpp:78:14: warning: variable 'i' set but not used [-Wunused-but-set-variable] + position_t i; + ^ +linearfickettaligner.cpp: In member function 's_alignment* LinearFickettAligner::align()': +linearfickettaligner.cpp:237:14: warning: variable 'minLen' set but not used [-Wunused-but-set-variable] + position_t minLen; + ^~~~~~ +linearfickettaligner.cpp: In member function 's_alignment* LinearFickettAligner::traceback(position_t, position_t)': +linearfickettaligner.cpp:344:14: warning: variable 'tlen' set but not used [-Wunused-but-set-variable] + position_t tlen; + ^~~~ +In file included from linearfickettaligner.cpp:25: +../include/linearfickettaligner.h: In instantiation of 'void LinearFickettAligner::LinearFickettTable::extendTable() [with T = int]': +../include/linearfickettaligner.h:70:11: required from 'void LinearFickettAligner::LinearFickettTable::reserve(count_t) [with T = int; count_t = unsigned int]' +linearfickettaligner.cpp:139:20: required from here +../include/linearfickettaligner.h:123:16: warning: variable 'size' set but not used [-Wunused-but-set-variable] + size_t size; + ^~~~ +../include/linearfickettaligner.h: In instantiation of 'void LinearFickettAligner::LinearFickettTable::extendTable() [with T = unsigned char]': +../include/linearfickettaligner.h:70:11: required from 'void LinearFickettAligner::LinearFickettTable::reserve(count_t) [with T = unsigned char; count_t = unsigned int]' +linearfickettaligner.cpp:142:26: required from here +../include/linearfickettaligner.h:123:16: warning: variable 'size' set but not used [-Wunused-but-set-variable] In file included from /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:277, from /usr/lib/i386-linux-gnu/openmpi/include/mpi.h:2684, from ../include/alignbounds.h:23, @@ -725,10 +788,17 @@ /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h:123:59: warning: cast between incompatible function types from 'void (*)(const void*, void*, int, const MPI::Datatype&)' to 'void (*)(void*, void*, int*, ompi_datatype_t**)' [-Wcast-function-type] ompi_op_set_cxx_callback(mpi_op, (MPI_User_function*) func); ^~~~ +mpic++ -DHAVE_CONFIG_H -I. -I.. -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O0 -ansi -pedantic -Wall -Wextra -Wno-long-long -Wno-unused-parameter -DHAVE_MPI_CPP -lm -g -O2 -ffile-prefix-map=/build/zalign-0.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/lib/openmpi/include -c -o mpialignmaster.o mpialignmaster.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O0 -ansi -pedantic -Wall -Wextra -Wno-long-long -Wno-unused-parameter -DHAVE_MPI_CPP -lm -g -O2 -ffile-prefix-map=/build/zalign-0.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/lib/openmpi/include -c -o mpialignslave.o mpialignslave.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O0 -ansi -pedantic -Wall -Wextra -Wno-long-long -Wno-unused-parameter -DHAVE_MPI_CPP -lm -g -O2 -ffile-prefix-map=/build/zalign-0.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/lib/openmpi/include -c -o opt.o opt.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O0 -ansi -pedantic -Wall -Wextra -Wno-long-long -Wno-unused-parameter -DHAVE_MPI_CPP -lm -g -O2 -ffile-prefix-map=/build/zalign-0.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/lib/openmpi/include -c -o score.o score.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O0 -ansi -pedantic -Wall -Wextra -Wno-long-long -Wno-unused-parameter -DHAVE_MPI_CPP -lm -g -O2 -ffile-prefix-map=/build/zalign-0.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/lib/openmpi/include -c -o sequence.o sequence.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O0 -ansi -pedantic -Wall -Wextra -Wno-long-long -Wno-unused-parameter -DHAVE_MPI_CPP -lm -g -O2 -ffile-prefix-map=/build/zalign-0.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/lib/openmpi/include -c -o limitsplotter.o limitsplotter.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O0 -ansi -pedantic -Wall -Wextra -Wno-long-long -Wno-unused-parameter -DHAVE_MPI_CPP -lm -g -O2 -ffile-prefix-map=/build/zalign-0.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/lib/openmpi/include -c -o zalign.o zalign.cpp In file included from /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:277, from /usr/lib/i386-linux-gnu/openmpi/include/mpi.h:2684, - from ../include/sequence.h:23, - from sequence.cpp:20: + from ../include/opt.h:23, + from opt.cpp:20: /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h: In member function 'virtual void MPI::Op::Init(void (*)(const void*, void*, int, const MPI::Datatype&), bool)': /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h:121:46: warning: cast between incompatible function types from 'void (*)(void*, void*, int*, ompi_datatype_t**, void (*)(void*, void*, int*, ompi_datatype_t**))' to 'void (*)(void*, void*, int*, ompi_datatype_t**)' [-Wcast-function-type] (void)MPI_Op_create((MPI_User_function*) ompi_mpi_cxx_op_intercept, @@ -738,9 +808,7 @@ ^~~~ In file included from /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:277, from /usr/lib/i386-linux-gnu/openmpi/include/mpi.h:2684, - from ../include/opt.h:23, - from ../include/fastareader.h:26, - from fastareader.cpp:20: + from mpialignmaster.cpp:22: /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h: In member function 'virtual void MPI::Op::Init(void (*)(const void*, void*, int, const MPI::Datatype&), bool)': /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h:121:46: warning: cast between incompatible function types from 'void (*)(void*, void*, int*, ompi_datatype_t**, void (*)(void*, void*, int*, ompi_datatype_t**))' to 'void (*)(void*, void*, int*, ompi_datatype_t**)' [-Wcast-function-type] (void)MPI_Op_create((MPI_User_function*) ompi_mpi_cxx_op_intercept, @@ -748,10 +816,6 @@ /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h:123:59: warning: cast between incompatible function types from 'void (*)(const void*, void*, int, const MPI::Datatype&)' to 'void (*)(void*, void*, int*, ompi_datatype_t**)' [-Wcast-function-type] ompi_op_set_cxx_callback(mpi_op, (MPI_User_function*) func); ^~~~ -linearfickettaligner.cpp: In member function 'void LinearFickettAligner::initializeFickettTable()': -linearfickettaligner.cpp:78:14: warning: variable 'i' set but not used [-Wunused-but-set-variable] - position_t i; - ^ In file included from /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:277, from /usr/lib/i386-linux-gnu/openmpi/include/mpi.h:2684, from ../include/alignbounds.h:23, @@ -763,30 +827,10 @@ /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h:123:59: warning: cast between incompatible function types from 'void (*)(const void*, void*, int, const MPI::Datatype&)' to 'void (*)(void*, void*, int*, ompi_datatype_t**)' [-Wcast-function-type] ompi_op_set_cxx_callback(mpi_op, (MPI_User_function*) func); ^~~~ -linearfickettaligner.cpp: In member function 's_alignment* LinearFickettAligner::align()': -linearfickettaligner.cpp:237:14: warning: variable 'minLen' set but not used [-Wunused-but-set-variable] - position_t minLen; - ^~~~~~ -linearfickettaligner.cpp: In member function 's_alignment* LinearFickettAligner::traceback(position_t, position_t)': -linearfickettaligner.cpp:344:14: warning: variable 'tlen' set but not used [-Wunused-but-set-variable] - position_t tlen; - ^~~~ -In file included from linearfickettaligner.cpp:25: -../include/linearfickettaligner.h: In instantiation of 'void LinearFickettAligner::LinearFickettTable::extendTable() [with T = int]': -../include/linearfickettaligner.h:70:11: required from 'void LinearFickettAligner::LinearFickettTable::reserve(count_t) [with T = int; count_t = unsigned int]' -linearfickettaligner.cpp:139:20: required from here -../include/linearfickettaligner.h:123:16: warning: variable 'size' set but not used [-Wunused-but-set-variable] - size_t size; - ^~~~ -../include/linearfickettaligner.h: In instantiation of 'void LinearFickettAligner::LinearFickettTable::extendTable() [with T = unsigned char]': -../include/linearfickettaligner.h:70:11: required from 'void LinearFickettAligner::LinearFickettTable::reserve(count_t) [with T = unsigned char; count_t = unsigned int]' -linearfickettaligner.cpp:142:26: required from here -../include/linearfickettaligner.h:123:16: warning: variable 'size' set but not used [-Wunused-but-set-variable] In file included from /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:277, from /usr/lib/i386-linux-gnu/openmpi/include/mpi.h:2684, - from ../include/alignbounds.h:23, - from ../include/zalign.h:31, - from zalign.cpp:20: + from ../include/sequence.h:23, + from sequence.cpp:20: /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h: In member function 'virtual void MPI::Op::Init(void (*)(const void*, void*, int, const MPI::Datatype&), bool)': /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h:121:46: warning: cast between incompatible function types from 'void (*)(void*, void*, int*, ompi_datatype_t**, void (*)(void*, void*, int*, ompi_datatype_t**))' to 'void (*)(void*, void*, int*, ompi_datatype_t**)' [-Wcast-function-type] (void)MPI_Op_create((MPI_User_function*) ompi_mpi_cxx_op_intercept, @@ -796,9 +840,9 @@ ^~~~ In file included from /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:277, from /usr/lib/i386-linux-gnu/openmpi/include/mpi.h:2684, - from ../include/blkseq.h:23, - from ../include/blkalign.h:26, - from blkalign.cpp:20: + from ../include/alignbounds.h:23, + from ../include/zalign.h:31, + from zalign.cpp:20: /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h: In member function 'virtual void MPI::Op::Init(void (*)(const void*, void*, int, const MPI::Datatype&), bool)': /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h:121:46: warning: cast between incompatible function types from 'void (*)(void*, void*, int*, ompi_datatype_t**, void (*)(void*, void*, int*, ompi_datatype_t**))' to 'void (*)(void*, void*, int*, ompi_datatype_t**)' [-Wcast-function-type] (void)MPI_Op_create((MPI_User_function*) ompi_mpi_cxx_op_intercept, @@ -806,8 +850,8 @@ /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h:123:59: warning: cast between incompatible function types from 'void (*)(const void*, void*, int, const MPI::Datatype&)' to 'void (*)(void*, void*, int*, ompi_datatype_t**)' [-Wcast-function-type] ompi_op_set_cxx_callback(mpi_op, (MPI_User_function*) func); ^~~~ -/bin/bash ../libtool --tag=CXX --mode=link mpic++ -g -O0 -ansi -pedantic -Wall -Wextra -Wno-long-long -Wno-unused-parameter -DHAVE_MPI_CPP -lm -g -O2 -ffile-prefix-map=/build/zalign-0.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/lib/openmpi/include -Wl,-z,relro -Wl,-z,now -o mpialign alignarray.o alignbounds.o alignment.o blkalign.o blkborder.o blkseq.o blkstrat.o fastareader.o linearfickettaligner.o mpialign.o mpialignmaster.o mpialignslave.o opt.o score.o sequence.o -/bin/bash ../libtool --tag=CXX --mode=link mpic++ -g -O0 -ansi -pedantic -Wall -Wextra -Wno-long-long -Wno-unused-parameter -DHAVE_MPI_CPP -lm -g -O2 -ffile-prefix-map=/build/zalign-0.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/lib/openmpi/include -Wl,-z,relro -Wl,-z,now -o zalign alignarray.o alignbounds.o alignment.o blkalign.o blkborder.o blkseq.o blkstrat.o fastareader.o limitsplotter.o linearfickettaligner.o opt.o score.o sequence.o zalign.o +/bin/sh ../libtool --tag=CXX --mode=link mpic++ -g -O0 -ansi -pedantic -Wall -Wextra -Wno-long-long -Wno-unused-parameter -DHAVE_MPI_CPP -lm -g -O2 -ffile-prefix-map=/build/zalign-0.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/lib/openmpi/include -Wl,-z,relro -Wl,-z,now -o mpialign alignarray.o alignbounds.o alignment.o blkalign.o blkborder.o blkseq.o blkstrat.o fastareader.o linearfickettaligner.o mpialign.o mpialignmaster.o mpialignslave.o opt.o score.o sequence.o +/bin/sh ../libtool --tag=CXX --mode=link mpic++ -g -O0 -ansi -pedantic -Wall -Wextra -Wno-long-long -Wno-unused-parameter -DHAVE_MPI_CPP -lm -g -O2 -ffile-prefix-map=/build/zalign-0.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/lib/openmpi/include -Wl,-z,relro -Wl,-z,now -o zalign alignarray.o alignbounds.o alignment.o blkalign.o blkborder.o blkseq.o blkstrat.o fastareader.o limitsplotter.o linearfickettaligner.o opt.o score.o sequence.o zalign.o libtool: link: mpic++ -g -O0 -ansi -pedantic -Wall -Wextra -Wno-long-long -Wno-unused-parameter -DHAVE_MPI_CPP -g -O2 -ffile-prefix-map=/build/zalign-0.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/lib/openmpi/include -Wl,-z -Wl,relro -Wl,-z -Wl,now -o zalign alignarray.o alignbounds.o alignment.o blkalign.o blkborder.o blkseq.o blkstrat.o fastareader.o limitsplotter.o linearfickettaligner.o opt.o score.o sequence.o zalign.o -lm libtool: link: mpic++ -g -O0 -ansi -pedantic -Wall -Wextra -Wno-long-long -Wno-unused-parameter -DHAVE_MPI_CPP -g -O2 -ffile-prefix-map=/build/zalign-0.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/lib/openmpi/include -Wl,-z -Wl,relro -Wl,-z -Wl,now -o mpialign alignarray.o alignbounds.o alignment.o blkalign.o blkborder.o blkseq.o blkstrat.o fastareader.o linearfickettaligner.o mpialign.o mpialignmaster.o mpialignslave.o opt.o score.o sequence.o -lm make[3]: Leaving directory '/build/zalign-0.9.1/src' @@ -816,7 +860,7 @@ make[2]: Leaving directory '/build/zalign-0.9.1' make[1]: Leaving directory '/build/zalign-0.9.1' dh_auto_test - make -j18 check VERBOSE=1 + make -j10 check VERBOSE=1 make[1]: Entering directory '/build/zalign-0.9.1' Making check in src make[2]: Entering directory '/build/zalign-0.9.1/src' @@ -836,8 +880,8 @@ Making install in src make[2]: Entering directory '/build/zalign-0.9.1/src' make[3]: Entering directory '/build/zalign-0.9.1/src' - /bin/mkdir -p '/build/zalign-0.9.1/debian/zalign/usr/bin' - /bin/bash ../libtool --mode=install /usr/bin/install -c mpialign zalign '/build/zalign-0.9.1/debian/zalign/usr/bin' + /usr/bin/mkdir -p '/build/zalign-0.9.1/debian/zalign/usr/bin' + /bin/sh ../libtool --mode=install /usr/bin/install -c mpialign zalign '/build/zalign-0.9.1/debian/zalign/usr/bin' libtool: install: /usr/bin/install -c mpialign /build/zalign-0.9.1/debian/zalign/usr/bin/mpialign libtool: install: /usr/bin/install -c zalign /build/zalign-0.9.1/debian/zalign/usr/bin/zalign make[3]: Nothing to be done for 'install-data-am'. @@ -862,7 +906,7 @@ dh_strip dh_makeshlibs dh_shlibdeps -dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/zalign/usr/bin/zalign debian/zalign/usr/bin/mpialign were not linked against libpthread.so.0 (they use none of the library's symbols) +dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/zalign/usr/bin/mpialign debian/zalign/usr/bin/zalign were not linked against libpthread.so.0 (they use none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums @@ -875,12 +919,14 @@ dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/6325/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/6325/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/10139 and its subdirectories -I: Current time: Fri Jul 24 12:12:57 -12 2020 -I: pbuilder-time-stamp: 1595635977 +I: removing directory /srv/workspace/pbuilder/6325 and its subdirectories +I: Current time: Sun Jun 23 08:01:53 +14 2019 +I: pbuilder-time-stamp: 1561226513