Diff of the two buildlogs: -- --- b1/build.log 2024-01-11 01:24:22.257429061 +0000 +++ b2/build.log 2024-01-11 01:34:58.811937643 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Jan 10 13:19:06 -12 2024 -I: pbuilder-time-stamp: 1704935946 +I: Current time: Thu Jan 11 15:28:12 +14 2024 +I: pbuilder-time-stamp: 1704936492 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: copying [./shapeit4_4.2.0+dfsg-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.46dvJNCn/trustedkeys.kbx': General error +gpgv: keyblock resource '/tmp/dpkg-verify-sig.wbi1Cxhm/trustedkeys.kbx': General error gpgv: Signature made Thu Feb 4 10:25:33 2021 gpgv: using RSA key 9A3C07BD06DE2F416E813A5D612EF1613E050F54 gpgv: issuer "daissi@debian.org" @@ -30,49 +30,80 @@ dpkg-source: info: applying use_shared_libs.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/16259/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/21778/tmp/hooks/D01_modify_environment starting +debug: Running on virt64b. +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 +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jan 11 01:28 /bin/sh -> /bin/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/21778/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/21778/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=3 ' - DISTRIBUTION='bullseye' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=4 ' + DIRSTACK=() + DISTRIBUTION=bullseye + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='2ef9dcef9b3b4bd9a544ac06d54abf3f' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='16259' - PS1='# ' - PS2='> ' + INVOCATION_ID=d0483a18622549b584e5cf14e093e6fb + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=21778 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.6Yd6gH2n/pbuilderrc_oH4E --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.6Yd6gH2n/b1 --logfile b1/build.log shapeit4_4.2.0+dfsg-1.dsc' - SUDO_GID='112' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.6Yd6gH2n/pbuilderrc_mLW5 --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.6Yd6gH2n/b2 --logfile b2/build.log shapeit4_4.2.0+dfsg-1.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt32b 6.1.0-17-armmp-lpae #1 SMP Debian 6.1.69-1 (2023-12-30) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-17-arm64 #1 SMP Debian 6.1.69-1 (2023-12-30) aarch64 GNU/Linux I: ls -l /bin total 3580 -rwxr-xr-x 1 root root 816764 Mar 27 2022 bash @@ -132,7 +163,7 @@ -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jan 7 09:26 sh -> dash + lrwxrwxrwx 1 root root 9 Jan 11 01:28 sh -> /bin/bash -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty -rwsr-xr-x 1 root root 46704 Jan 20 2022 su @@ -158,7 +189,7 @@ -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew -I: user script /srv/workspace/pbuilder/16259/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/21778/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -260,7 +291,7 @@ Get: 56 http://deb.debian.org/debian bullseye/main armhf liblzma-dev armhf 5.2.5-2.1~deb11u1 [220 kB] Get: 57 http://deb.debian.org/debian bullseye/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2+deb11u2 [185 kB] Get: 58 http://deb.debian.org/debian bullseye/main armhf libhts-dev armhf 1.11-4 [3819 kB] -Fetched 45.1 MB in 4s (11.5 MB/s) +Fetched 45.1 MB in 4s (10.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 17486 files and directories currently installed.) @@ -508,7 +539,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/shapeit4-4.2.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../shapeit4_4.2.0+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/21778/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/21778/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/shapeit4-4.2.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../shapeit4_4.2.0+dfsg-1_source.changes dpkg-buildpackage: info: source package shapeit4 dpkg-buildpackage: info: source version 4.2.0+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -518,7 +553,7 @@ debian/rules clean dh clean dh_auto_clean - make -j3 clean + make -j4 clean make[1]: Entering directory '/build/reproducible-path/shapeit4-4.2.0+dfsg' rm -f obj/*.o bin/shapeit4.2 make[1]: Leaving directory '/build/reproducible-path/shapeit4-4.2.0+dfsg' @@ -529,39 +564,33 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j3 "INSTALL=install --strip-program=true" + make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/shapeit4-4.2.0+dfsg' -g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/models/haplotype_segment_single.cpp -o obj/haplotype_segment_single.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/models/haplotype_segment_double.cpp -o obj/haplotype_segment_double.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include -g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/containers/bitmatrix.cpp -o obj/bitmatrix.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include -In file included from src/containers/bitmatrix.cpp:22: +g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/models/haplotype_segment_single.cpp -o obj/haplotype_segment_single.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include +g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/modules/builder.cpp -o obj/builder.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include +g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/modules/pbwt_solver.cpp -o obj/pbwt_solver.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include +In file included from src/containers/haplotype_set.h:27, + from src/objects/compute_job.h:27, + from src/models/haplotype_segment_single.h:26, + from src/models/haplotype_segment_single.cpp:22: src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)': src/containers/bitmatrix.h:28:109: warning: right shift count >= width of type [-Wshift-count-overflow] 28 | return static_cast((static_cast(i1) * static_cast(i2)) >> 32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from src/containers/haplotype_set.h:27, - from src/objects/compute_job.h:27, - from src/models/haplotype_segment_double.h:26, - from src/models/haplotype_segment_double.cpp:22: + from src/modules/pbwt_solver.h:26, + from src/modules/pbwt_solver.cpp:22: src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)': src/containers/bitmatrix.h:28:109: warning: right shift count >= width of type [-Wshift-count-overflow] 28 | return static_cast((static_cast(i1) * static_cast(i2)) >> 32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -In file included from src/objects/compute_job.h:27, - from src/models/haplotype_segment_double.h:26, - from src/models/haplotype_segment_double.cpp:22: +In file included from src/modules/pbwt_solver.h:26, + from src/modules/pbwt_solver.cpp:22: src/containers/haplotype_set.h: In member function 'bool IBD2track::merge(const IBD2track&)': src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type] 53 | } | ^ -In file included from src/containers/haplotype_set.h:27, - from src/objects/compute_job.h:27, - from src/models/haplotype_segment_single.h:26, - from src/models/haplotype_segment_single.cpp:22: -src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)': -src/containers/bitmatrix.h:28:109: warning: right shift count >= width of type [-Wshift-count-overflow] - 28 | return static_cast((static_cast(i1) * static_cast(i2)) >> 32); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from src/objects/compute_job.h:27, from src/models/haplotype_segment_single.h:26, from src/models/haplotype_segment_single.cpp:22: @@ -569,39 +598,50 @@ src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type] 53 | } | ^ -g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/containers/haplotype_set.cpp -o obj/haplotype_set.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include -g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/containers/variant_map.cpp -o obj/variant_map.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include +src/modules/pbwt_solver.cpp: In member function 'void pbwt_solver::sweep(genotype_set&)': +src/modules/pbwt_solver.cpp:93:57: warning: overflow in conversion from 'double' to '__gnu_cxx::__alloc_traits, char>::value_type' {aka 'char'} changes value from '-1.0e+0' to '0' [-Woverflow] + 93 | if (s > thresh) { Guess[h+0] = 1.0; Guess[h+1] = -1.0; Amb[i] = false; } + | ^~~~ +src/modules/pbwt_solver.cpp:94:45: warning: overflow in conversion from 'double' to '__gnu_cxx::__alloc_traits, char>::value_type' {aka 'char'} changes value from '-1.0e+0' to '0' [-Woverflow] + 94 | else if (s < -thresh) { Guess[h+0] = -1.0; Guess[h+1] = 1.0; Amb[i] = false; } + | ^~~~ +src/modules/pbwt_solver.cpp:103:49: warning: overflow in conversion from 'double' to '__gnu_cxx::__alloc_traits, char>::value_type' {aka 'char'} changes value from '-1.0e+0' to '0' [-Woverflow] + 103 | if (s0 == -2 && s1 == -2) { Guess[h+0] = -1.0; Guess[h+1] = -1.0; Amb[i] = false; } + | ^~~~ +src/modules/pbwt_solver.cpp:103:68: warning: overflow in conversion from 'double' to '__gnu_cxx::__alloc_traits, char>::value_type' {aka 'char'} changes value from '-1.0e+0' to '0' [-Woverflow] + 103 | if (s0 == -2 && s1 == -2) { Guess[h+0] = -1.0; Guess[h+1] = -1.0; Amb[i] = false; } + | ^~~~ +src/modules/pbwt_solver.cpp:104:53: warning: overflow in conversion from 'double' to '__gnu_cxx::__alloc_traits, char>::value_type' {aka 'char'} changes value from '-1.0e+0' to '0' [-Woverflow] + 104 | else if (s0 == -2 && s1 == 2) { Guess[h+0] = -1.0; Guess[h+1] = 1.0; Amb[i] = false; } + | ^~~~ +src/modules/pbwt_solver.cpp:105:71: warning: overflow in conversion from 'double' to '__gnu_cxx::__alloc_traits, char>::value_type' {aka 'char'} changes value from '-1.0e+0' to '0' [-Woverflow] + 105 | else if (s0 == 2 && s1 == -2) { Guess[h+0] = 1.0; Guess[h+1] = -1.0; Amb[i] = false; } + | ^~~~ +src/modules/pbwt_solver.cpp:134:26: warning: overflow in conversion from 'double' to '__gnu_cxx::__alloc_traits, char>::value_type' {aka 'char'} changes value from '-1.0e+0' to '0' [-Woverflow] + 134 | else Guess[h+0] = -1.0; + | ^~~~ +src/modules/pbwt_solver.cpp:136:26: warning: overflow in conversion from 'double' to '__gnu_cxx::__alloc_traits, char>::value_type' {aka 'char'} changes value from '-1.0e+0' to '0' [-Woverflow] + 136 | else Guess[h+1] = -1.0; + | ^~~~ In file included from src/containers/haplotype_set.h:27, - from src/containers/haplotype_set.cpp:22: + from src/objects/compute_job.h:27, + from src/models/haplotype_segment_double.h:26, + from src/models/haplotype_segment_double.cpp:22: src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)': src/containers/bitmatrix.h:28:109: warning: right shift count >= width of type [-Wshift-count-overflow] 28 | return static_cast((static_cast(i1) * static_cast(i2)) >> 32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -In file included from src/containers/haplotype_set.cpp:22: +In file included from src/objects/compute_job.h:27, + from src/models/haplotype_segment_double.h:26, + from src/models/haplotype_segment_double.cpp:22: src/containers/haplotype_set.h: In member function 'bool IBD2track::merge(const IBD2track&)': src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type] 53 | } | ^ -g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/containers/genotype_set.cpp -o obj/genotype_set.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include -In file included from /usr/include/c++/10/vector:72, - from src/utils/otools.h:26, - from src/containers/haplotype_set.h:25, - from src/containers/haplotype_set.cpp:22: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from src/utils/otools.h:26, - from src/containers/haplotype_set.h:25, - from src/containers/haplotype_set.cpp:22: -/usr/include/c++/10/bits/stl_vector.h: In member function 'void haplotype_set::initializePBWTmapping(variant_map&)': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/main.cpp -o obj/main.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include -g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/io/haplotype_writer.cpp -o obj/haplotype_writer.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include -g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/io/gmap_reader.cpp -o obj/gmap_reader.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include +g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/containers/haplotype_set.cpp -o obj/haplotype_set.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include +g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/containers/bitmatrix.cpp -o obj/bitmatrix.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include +g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/containers/variant_map.cpp -o obj/variant_map.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include In file included from src/containers/haplotype_set.h:27, from src/objects/compute_job.h:27, from src/models/haplotype_segment_single.h:26, @@ -620,73 +660,149 @@ 53 | } | ^ In file included from src/containers/haplotype_set.h:27, - from src/io/haplotype_writer.h:28, - from src/io/haplotype_writer.cpp:22: + from src/containers/haplotype_set.cpp:22: src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)': src/containers/bitmatrix.h:28:109: warning: right shift count >= width of type [-Wshift-count-overflow] 28 | return static_cast((static_cast(i1) * static_cast(i2)) >> 32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -In file included from src/io/haplotype_writer.h:28, - from src/io/haplotype_writer.cpp:22: +In file included from src/containers/haplotype_set.cpp:22: src/containers/haplotype_set.h: In member function 'bool IBD2track::merge(const IBD2track&)': src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type] 53 | } | ^ -g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/io/genotype_reader1.cpp -o obj/genotype_reader1.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include -src/io/haplotype_writer.cpp: In member function 'void haplotype_writer::writeHaplotypes(std::string)': -src/io/haplotype_writer.cpp:59:15: warning: ignoring return value of 'int bcf_hdr_write(htsFile*, bcf_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 59 | bcf_hdr_write(fp, hdr); - | ~~~~~~~~~~~~~^~~~~~~~~ -g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/io/graph_writer.cpp -o obj/graph_writer.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include +g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/containers/genotype_set.cpp -o obj/genotype_set.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include +In file included from src/containers/bitmatrix.cpp:22: +src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)': +src/containers/bitmatrix.h:28:109: warning: right shift count >= width of type [-Wshift-count-overflow] + 28 | return static_cast((static_cast(i1) * static_cast(i2)) >> 32); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /usr/include/c++/10/vector:72, from src/utils/otools.h:26, - from src/io/gmap_reader.h:25, - from src/io/gmap_reader.cpp:23: + from src/containers/haplotype_set.h:25, + from src/containers/haplotype_set.cpp:22: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from src/containers/haplotype_set.h:27, - from src/io/genotype_reader.h:28, - from src/io/genotype_reader1.cpp:22: -src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)': -src/containers/bitmatrix.h:28:109: warning: right shift count >= width of type [-Wshift-count-overflow] - 28 | return static_cast((static_cast(i1) * static_cast(i2)) >> 32); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -In file included from src/io/genotype_reader.h:28, - from src/io/genotype_reader1.cpp:22: -src/containers/haplotype_set.h: In member function 'bool IBD2track::merge(const IBD2track&)': -src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type] - 53 | } - | ^ +g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/hmm_parameters.cpp -o obj/hmm_parameters.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include In file included from /usr/include/c++/10/vector:67, from src/utils/otools.h:26, - from src/io/gmap_reader.h:25, - from src/io/gmap_reader.cpp:23: -/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmap_reader::readGeneticMapFile(std::string)': + from src/containers/haplotype_set.h:25, + from src/containers/haplotype_set.cpp:22: +/usr/include/c++/10/bits/stl_vector.h: In member function 'void haplotype_set::initializePBWTmapping(variant_map&)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/io/genotype_reader2.cpp -o obj/genotype_reader2.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include -g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/phaser/phaser_management.cpp -o obj/phaser_management.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include +g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/compute_job.cpp -o obj/compute_job.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include +g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/genotype/genotype_prune.cpp -o obj/genotype_prune.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include +g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/genotype/genotype_managment.cpp -o obj/genotype_managment.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include In file included from src/containers/haplotype_set.h:27, - from src/io/genotype_reader.h:28, - from src/io/genotype_reader2.cpp:22: + from src/objects/compute_job.h:27, + from src/objects/compute_job.cpp:22: src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)': src/containers/bitmatrix.h:28:109: warning: right shift count >= width of type [-Wshift-count-overflow] 28 | return static_cast((static_cast(i1) * static_cast(i2)) >> 32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -In file included from src/io/genotype_reader.h:28, - from src/io/genotype_reader2.cpp:22: +In file included from src/objects/compute_job.h:27, + from src/objects/compute_job.cpp:22: src/containers/haplotype_set.h: In member function 'bool IBD2track::merge(const IBD2track&)': src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type] 53 | } | ^ +g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/genotype/genotype_mask.cpp -o obj/genotype_mask.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include +In file included from /usr/include/c++/10/queue:62, + from src/utils/otools.h:28, + from src/objects/genotype/genotype_header.h:25, + from src/objects/genotype/genotype_prune.cpp:22: +/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = TransStatistics; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = Transition; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In file included from /usr/include/c++/10/algorithm:62, + from src/utils/otools.h:35, + from src/objects/genotype/genotype_header.h:25, + from src/objects/genotype/genotype_prune.cpp:22: +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1839 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1945 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/genotype/genotype_build.cpp -o obj/genotype_build.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1945 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h: In member function 'void genotype::mapMerges(std::vector&, double, std::vector&)': +/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1974 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1975 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1976 | __comp); + | ~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1891 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1974 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1975 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1976 | __comp); + | ~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1891 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h: In member function 'void genotype::performMerges(std::vector&, std::vector&)': +/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1974 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1975 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1976 | __comp); + | ~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1891 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/genotype/genotype_sweep.cpp -o obj/genotype_sweep.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include +g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/variant.cpp -o obj/variant.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include +g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/phaser/phaser_algorithm.cpp -o obj/phaser_algorithm.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include +g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/phaser/phaser_management.cpp -o obj/phaser_management.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include +g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/phaser/phaser_finalise.cpp -o obj/phaser_finalise.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include In file included from src/containers/haplotype_set.h:27, from src/objects/compute_job.h:27, from src/models/haplotype_segment_single.h:26, from src/phaser/phaser_header.h:29, - from src/phaser/phaser_management.cpp:22: + from src/phaser/phaser_algorithm.cpp:22: src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)': src/containers/bitmatrix.h:28:109: warning: right shift count >= width of type [-Wshift-count-overflow] 28 | return static_cast((static_cast(i1) * static_cast(i2)) >> 32); @@ -694,18 +810,16 @@ In file included from src/objects/compute_job.h:27, from src/models/haplotype_segment_single.h:26, from src/phaser/phaser_header.h:29, - from src/phaser/phaser_management.cpp:22: + from src/phaser/phaser_algorithm.cpp:22: src/containers/haplotype_set.h: In member function 'bool IBD2track::merge(const IBD2track&)': src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type] 53 | } | ^ -g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/phaser/phaser_initialise.cpp -o obj/phaser_initialise.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include -g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/phaser/phaser_finalise.cpp -o obj/phaser_finalise.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include In file included from src/containers/haplotype_set.h:27, from src/objects/compute_job.h:27, from src/models/haplotype_segment_single.h:26, from src/phaser/phaser_header.h:29, - from src/phaser/phaser_initialise.cpp:22: + from src/phaser/phaser_management.cpp:22: src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)': src/containers/bitmatrix.h:28:109: warning: right shift count >= width of type [-Wshift-count-overflow] 28 | return static_cast((static_cast(i1) * static_cast(i2)) >> 32); @@ -713,11 +827,12 @@ In file included from src/objects/compute_job.h:27, from src/models/haplotype_segment_single.h:26, from src/phaser/phaser_header.h:29, - from src/phaser/phaser_initialise.cpp:22: + from src/phaser/phaser_management.cpp:22: src/containers/haplotype_set.h: In member function 'bool IBD2track::merge(const IBD2track&)': src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type] 53 | } | ^ +g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/phaser/phaser_parameters.cpp -o obj/phaser_parameters.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include In file included from src/containers/haplotype_set.h:27, from src/objects/compute_job.h:27, from src/models/haplotype_segment_single.h:26, @@ -735,14 +850,13 @@ src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type] 53 | } | ^ -g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/phaser/phaser_algorithm.cpp -o obj/phaser_algorithm.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include -g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/phaser/phaser_parameters.cpp -o obj/phaser_parameters.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include -g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/modules/builder.cpp -o obj/builder.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include +g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/phaser/phaser_initialise.cpp -o obj/phaser_initialise.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include +g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/io/haplotype_writer.cpp -o obj/haplotype_writer.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include In file included from src/containers/haplotype_set.h:27, from src/objects/compute_job.h:27, from src/models/haplotype_segment_single.h:26, from src/phaser/phaser_header.h:29, - from src/phaser/phaser_algorithm.cpp:22: + from src/phaser/phaser_parameters.cpp:23: src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)': src/containers/bitmatrix.h:28:109: warning: right shift count >= width of type [-Wshift-count-overflow] 28 | return static_cast((static_cast(i1) * static_cast(i2)) >> 32); @@ -750,16 +864,17 @@ In file included from src/objects/compute_job.h:27, from src/models/haplotype_segment_single.h:26, from src/phaser/phaser_header.h:29, - from src/phaser/phaser_algorithm.cpp:22: + from src/phaser/phaser_parameters.cpp:23: src/containers/haplotype_set.h: In member function 'bool IBD2track::merge(const IBD2track&)': src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type] 53 | } | ^ +g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/io/genotype_reader2.cpp -o obj/genotype_reader2.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include In file included from src/containers/haplotype_set.h:27, from src/objects/compute_job.h:27, from src/models/haplotype_segment_single.h:26, from src/phaser/phaser_header.h:29, - from src/phaser/phaser_parameters.cpp:23: + from src/phaser/phaser_initialise.cpp:22: src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)': src/containers/bitmatrix.h:28:109: warning: right shift count >= width of type [-Wshift-count-overflow] 28 | return static_cast((static_cast(i1) * static_cast(i2)) >> 32); @@ -767,154 +882,74 @@ In file included from src/objects/compute_job.h:27, from src/models/haplotype_segment_single.h:26, from src/phaser/phaser_header.h:29, - from src/phaser/phaser_parameters.cpp:23: + from src/phaser/phaser_initialise.cpp:22: src/containers/haplotype_set.h: In member function 'bool IBD2track::merge(const IBD2track&)': src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type] 53 | } | ^ -g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/modules/pbwt_solver.cpp -o obj/pbwt_solver.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include -g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/variant.cpp -o obj/variant.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include In file included from src/containers/haplotype_set.h:27, - from src/modules/pbwt_solver.h:26, - from src/modules/pbwt_solver.cpp:22: + from src/io/haplotype_writer.h:28, + from src/io/haplotype_writer.cpp:22: src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)': src/containers/bitmatrix.h:28:109: warning: right shift count >= width of type [-Wshift-count-overflow] 28 | return static_cast((static_cast(i1) * static_cast(i2)) >> 32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -In file included from src/modules/pbwt_solver.h:26, - from src/modules/pbwt_solver.cpp:22: +In file included from src/io/haplotype_writer.h:28, + from src/io/haplotype_writer.cpp:22: src/containers/haplotype_set.h: In member function 'bool IBD2track::merge(const IBD2track&)': src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type] 53 | } | ^ -src/modules/pbwt_solver.cpp: In member function 'void pbwt_solver::sweep(genotype_set&)': -src/modules/pbwt_solver.cpp:93:57: warning: overflow in conversion from 'double' to '__gnu_cxx::__alloc_traits, char>::value_type' {aka 'char'} changes value from '-1.0e+0' to '0' [-Woverflow] - 93 | if (s > thresh) { Guess[h+0] = 1.0; Guess[h+1] = -1.0; Amb[i] = false; } - | ^~~~ -src/modules/pbwt_solver.cpp:94:45: warning: overflow in conversion from 'double' to '__gnu_cxx::__alloc_traits, char>::value_type' {aka 'char'} changes value from '-1.0e+0' to '0' [-Woverflow] - 94 | else if (s < -thresh) { Guess[h+0] = -1.0; Guess[h+1] = 1.0; Amb[i] = false; } - | ^~~~ -src/modules/pbwt_solver.cpp:103:49: warning: overflow in conversion from 'double' to '__gnu_cxx::__alloc_traits, char>::value_type' {aka 'char'} changes value from '-1.0e+0' to '0' [-Woverflow] - 103 | if (s0 == -2 && s1 == -2) { Guess[h+0] = -1.0; Guess[h+1] = -1.0; Amb[i] = false; } - | ^~~~ -src/modules/pbwt_solver.cpp:103:68: warning: overflow in conversion from 'double' to '__gnu_cxx::__alloc_traits, char>::value_type' {aka 'char'} changes value from '-1.0e+0' to '0' [-Woverflow] - 103 | if (s0 == -2 && s1 == -2) { Guess[h+0] = -1.0; Guess[h+1] = -1.0; Amb[i] = false; } - | ^~~~ -src/modules/pbwt_solver.cpp:104:53: warning: overflow in conversion from 'double' to '__gnu_cxx::__alloc_traits, char>::value_type' {aka 'char'} changes value from '-1.0e+0' to '0' [-Woverflow] - 104 | else if (s0 == -2 && s1 == 2) { Guess[h+0] = -1.0; Guess[h+1] = 1.0; Amb[i] = false; } - | ^~~~ -src/modules/pbwt_solver.cpp:105:71: warning: overflow in conversion from 'double' to '__gnu_cxx::__alloc_traits, char>::value_type' {aka 'char'} changes value from '-1.0e+0' to '0' [-Woverflow] - 105 | else if (s0 == 2 && s1 == -2) { Guess[h+0] = 1.0; Guess[h+1] = -1.0; Amb[i] = false; } - | ^~~~ -src/modules/pbwt_solver.cpp:134:26: warning: overflow in conversion from 'double' to '__gnu_cxx::__alloc_traits, char>::value_type' {aka 'char'} changes value from '-1.0e+0' to '0' [-Woverflow] - 134 | else Guess[h+0] = -1.0; - | ^~~~ -src/modules/pbwt_solver.cpp:136:26: warning: overflow in conversion from 'double' to '__gnu_cxx::__alloc_traits, char>::value_type' {aka 'char'} changes value from '-1.0e+0' to '0' [-Woverflow] - 136 | else Guess[h+1] = -1.0; - | ^~~~ -g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/compute_job.cpp -o obj/compute_job.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include -g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/genotype/genotype_mask.cpp -o obj/genotype_mask.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include -g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/genotype/genotype_build.cpp -o obj/genotype_build.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include In file included from src/containers/haplotype_set.h:27, - from src/objects/compute_job.h:27, - from src/objects/compute_job.cpp:22: + from src/io/genotype_reader.h:28, + from src/io/genotype_reader2.cpp:22: src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)': src/containers/bitmatrix.h:28:109: warning: right shift count >= width of type [-Wshift-count-overflow] 28 | return static_cast((static_cast(i1) * static_cast(i2)) >> 32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -In file included from src/objects/compute_job.h:27, - from src/objects/compute_job.cpp:22: +In file included from src/io/genotype_reader.h:28, + from src/io/genotype_reader2.cpp:22: src/containers/haplotype_set.h: In member function 'bool IBD2track::merge(const IBD2track&)': src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type] 53 | } | ^ -g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/genotype/genotype_managment.cpp -o obj/genotype_managment.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include -g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/genotype/genotype_sweep.cpp -o obj/genotype_sweep.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include -g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/genotype/genotype_prune.cpp -o obj/genotype_prune.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include -g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/hmm_parameters.cpp -o obj/hmm_parameters.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include -In file included from /usr/include/c++/10/queue:62, - from src/utils/otools.h:28, - from src/objects/genotype/genotype_header.h:25, - from src/objects/genotype/genotype_prune.cpp:22: -/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = TransStatistics; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = Transition; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In file included from /usr/include/c++/10/algorithm:62, - from src/utils/otools.h:35, - from src/objects/genotype/genotype_header.h:25, - from src/objects/genotype/genotype_prune.cpp:22: -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1839 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1945 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1945 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h: In member function 'void genotype::mapMerges(std::vector&, double, std::vector&)': -/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1974 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1975 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1976 | __comp); - | ~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1891 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1974 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1975 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1976 | __comp); - | ~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1891 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h: In member function 'void genotype::performMerges(std::vector&, std::vector&)': -/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1974 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1975 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1976 | __comp); - | ~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1891 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -std=c++11 -Wl,-z,relro -Wl,-z,now -O3 obj/haplotype_segment_single.o obj/haplotype_segment_double.o obj/bitmatrix.o obj/haplotype_set.o obj/variant_map.o obj/genotype_set.o obj/main.o obj/haplotype_writer.o obj/gmap_reader.o obj/genotype_reader1.o obj/graph_writer.o obj/genotype_reader2.o obj/phaser_management.o obj/phaser_initialise.o obj/phaser_finalise.o obj/phaser_algorithm.o obj/phaser_parameters.o obj/builder.o obj/pbwt_solver.o obj/variant.o obj/compute_job.o obj/genotype_mask.o obj/genotype_build.o obj/genotype_managment.o obj/genotype_sweep.o obj/genotype_prune.o obj/hmm_parameters.o -lhts -lboost_iostreams -lboost_program_options -o bin/shapeit4.2 -lz -lbz2 -lm -lpthread -llzma +src/io/haplotype_writer.cpp: In member function 'void haplotype_writer::writeHaplotypes(std::string)': +src/io/haplotype_writer.cpp:59:15: warning: ignoring return value of 'int bcf_hdr_write(htsFile*, bcf_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 59 | bcf_hdr_write(fp, hdr); + | ~~~~~~~~~~~~~^~~~~~~~~ +g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/io/genotype_reader1.cpp -o obj/genotype_reader1.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include +g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/io/graph_writer.cpp -o obj/graph_writer.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include +In file included from src/containers/haplotype_set.h:27, + from src/io/genotype_reader.h:28, + from src/io/genotype_reader1.cpp:22: +src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)': +src/containers/bitmatrix.h:28:109: warning: right shift count >= width of type [-Wshift-count-overflow] + 28 | return static_cast((static_cast(i1) * static_cast(i2)) >> 32); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +In file included from src/io/genotype_reader.h:28, + from src/io/genotype_reader1.cpp:22: +src/containers/haplotype_set.h: In member function 'bool IBD2track::merge(const IBD2track&)': +src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type] + 53 | } + | ^ +g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/io/gmap_reader.cpp -o obj/gmap_reader.o -Isrc -I/build/reproducible-path/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include +In file included from /usr/include/c++/10/vector:72, + from src/utils/otools.h:26, + from src/io/gmap_reader.h:25, + from src/io/gmap_reader.cpp:23: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, + from src/utils/otools.h:26, + from src/io/gmap_reader.h:25, + from src/io/gmap_reader.cpp:23: +/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmap_reader::readGeneticMapFile(std::string)': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +g++ -std=c++11 -Wl,-z,relro -Wl,-z,now -O3 obj/haplotype_segment_double.o obj/haplotype_segment_single.o obj/builder.o obj/pbwt_solver.o obj/main.o obj/haplotype_set.o obj/bitmatrix.o obj/variant_map.o obj/genotype_set.o obj/hmm_parameters.o obj/compute_job.o obj/genotype_prune.o obj/genotype_managment.o obj/genotype_mask.o obj/genotype_build.o obj/genotype_sweep.o obj/variant.o obj/phaser_algorithm.o obj/phaser_management.o obj/phaser_finalise.o obj/phaser_parameters.o obj/phaser_initialise.o obj/haplotype_writer.o obj/genotype_reader2.o obj/genotype_reader1.o obj/graph_writer.o obj/gmap_reader.o -lhts -lboost_iostreams -lboost_program_options -o bin/shapeit4.2 -lz -lbz2 -lm -lpthread -llzma make[1]: Leaving directory '/build/reproducible-path/shapeit4-4.2.0+dfsg' dh_auto_test create-stamp debian/debhelper-build-stamp @@ -949,12 +984,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/21778/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/21778/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/16259 and its subdirectories -I: Current time: Wed Jan 10 13:24:18 -12 2024 -I: pbuilder-time-stamp: 1704936258 +I: removing directory /srv/workspace/pbuilder/21778 and its subdirectories +I: Current time: Thu Jan 11 15:34:54 +14 2024 +I: pbuilder-time-stamp: 1704936894