Diff of the two buildlogs: -- --- b1/build.log 2024-12-20 00:01:18.488951180 +0000 +++ b2/build.log 2024-12-20 00:04:11.377081215 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Jan 21 18:21:46 -12 2026 -I: pbuilder-time-stamp: 1769062906 +I: Current time: Fri Dec 20 14:01:25 +14 2024 +I: pbuilder-time-stamp: 1734652885 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -32,52 +32,84 @@ dpkg-source: info: applying gcc-4.1.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3459881/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3702951/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +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 Dec 20 00:01 /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/3702951/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3702951/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='cea03d0b357b4b9ca21b648f190ca873' - 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='3459881' - PS1='# ' - PS2='> ' + INVOCATION_ID=5e821bbb5fd3430b817483faadfbb209 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + 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=3702951 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.dnjIMHtp/pbuilderrc_lnkj --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.dnjIMHtp/b1 --logfile b1/build.log loki_2.4.7.4-12.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.dnjIMHtp/pbuilderrc_cBwB --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.dnjIMHtp/b2 --logfile b2/build.log loki_2.4.7.4-12.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3459881/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3702951/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -142,7 +174,7 @@ Get: 27 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.22 [919 kB] -Fetched 19.8 MB in 1s (34.8 MB/s) +Fetched 19.8 MB in 3s (6969 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 19967 files and directories currently installed.) @@ -273,7 +305,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/loki-2.4.7.4/ && 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 > ../loki_2.4.7.4-12_source.changes +I: user script /srv/workspace/pbuilder/3702951/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3702951/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/loki-2.4.7.4/ && 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 > ../loki_2.4.7.4-12_source.changes dpkg-buildpackage: info: source package loki dpkg-buildpackage: info: source version 2.4.7.4-12 dpkg-buildpackage: info: source distribution unstable @@ -394,7 +430,7 @@ # nothing to do here make[1]: Leaving directory '/build/reproducible-path/loki-2.4.7.4' dh_auto_build -Nloki-doc - make -j42 + make -j20 make[1]: Entering directory '/build/reproducible-path/loki-2.4.7.4' for subdir in libsrc prepsrc lokisrc utils; do \ (cd $subdir; make depend) \ @@ -455,8 +491,6 @@ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gen_elim.o gen_elim.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prep_do_peel_op.o prep_do_peel_op.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o write_data.o write_data.c -lex.yy.c:2062:12: warning: 'input' defined but not used [-Wunused-function] -write_report.c: In function 'WriteReport': setup_ped.c: In function 'setup_pedigree': setup_ped.c:426:83: warning: this statement may fall through [-Wimplicit-fallthrough=] 426 | if(i!=id) { @@ -464,16 +498,7 @@ setup_ped.c:430:74: note: here 430 | default: | ^~~~~~~ -write_report.c:286:28: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses] - 286 | if(!elem->type&(ST_MODEL|ST_TRAIT)) continue; - | ^~~~~~~~~~~ -write_report.c:300:28: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses] - 300 | if(!elem->type&(ST_MODEL|ST_TRAIT)) continue; - | ^~~~~~~~~~~ -prep_do_peel_op.c: In function 'do_peel_op': -prep_do_peel_op.c:238:26: warning: variable 'fill' set but not used [-Wunused-but-set-variable] - 238 | double max_terms,fill; - | ^~~~ +lex.yy.c:2062:12: warning: 'input' defined but not used [-Wunused-function] setup_ped.c: In function 'check_ymark': setup_ped.c:1135:42: warning: pointer 'list' may be used after 'free' [-Wuse-after-free] 1135 | if(pl->type==LINK_Y) list[ny++]=locus; @@ -487,6 +512,13 @@ setup_ped.c:1127:9: note: call to 'free' here 1127 | free(list); | ^~~~~~~~~~ +write_report.c: In function 'WriteReport': +write_report.c:286:28: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses] + 286 | if(!elem->type&(ST_MODEL|ST_TRAIT)) continue; + | ^~~~~~~~~~~ +write_report.c:300:28: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses] + 300 | if(!elem->type&(ST_MODEL|ST_TRAIT)) continue; + | ^~~~~~~~~~~ gen_elim.c: In function 'min_degree': gen_elim.c:1075:31: warning: variable 'best_fg' set but not used [-Wunused-but-set-variable] 1075 | int x,i1,k1,k2,*trans,best_fg=0; @@ -505,6 +537,10 @@ gen_elim.c:1266:34: warning: variable 'pp1' set but not used [-Wunused-but-set-variable] 1266 | struct Peelseq_Head *pp,*pp1; | ^~~ +prep_do_peel_op.c: In function 'do_peel_op': +prep_do_peel_op.c:238:26: warning: variable 'fill' set but not used [-Wunused-but-set-variable] + 238 | double max_terms,fill; + | ^~~~ control_lex.l: In function 'yy_orig_lex': control_lex.l:106:11: warning: '__builtin_strncpy' specified bound 4096 equals destination size [-Wstringop-truncation] 106 | (void)strncpy(linebuf,yytext+1,LINEBUFSIZE); @@ -555,39 +591,21 @@ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_pen.o loki_pen.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_tlmoves.o loki_tlmoves.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o meiosis_scan.o meiosis_scan.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_identity.o loki_identity.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample_rand.o sample_rand.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample_effects.o sample_effects.c -param_lex.c: In function 'yy_get_next_buffer': -param_lex.c:641:32: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] - 641 | for ( n = 0; n < max_size && \ - | ^ -param_lex.c:1161:17: note: in expansion of macro 'YY_INPUT' - 1161 | YY_INPUT( (&YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[number_to_move]), - | ^~~~~~~~ -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_setup.o loki_setup.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_dump.o loki_dump.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample_cens.o sample_cens.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o handle_res.o handle_res.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o print_data.o print_data.c -param_lex.c: At top level: -param_lex.c:1301:16: warning: 'input' defined but not used [-Wunused-function] - 1301 | static int input (void) - | ^~~~~ -param_lex.c:1260:17: warning: 'yyunput' defined but not used [-Wunused-function] - 1260 | static void yyunput (int c, register char * yy_bp ) - | ^~~~~~~ -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o calc_var_locus.o calc_var_locus.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_output.o loki_output.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample_nu.o sample_nu.c pass_founder_genes.c: In function 'pass_founder_genes': pass_founder_genes.c:35:47: warning: variable 'locus1' set but not used [-Wunused-but-set-variable] 35 | int i,i1,j,s,**genes,**seg,comp,cs,nc,locus1; | ^~~~~~ -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_complex_peel.o loki_complex_peel.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_npl.o loki_npl.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_simple_sample.o loki_simple_sample.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_simple_peel.o loki_simple_peel.c +gen_pen.c: In function 'calc_degree': +gen_pen.c:321:31: warning: variable 'k2' set but not used [-Wunused-but-set-variable] + 321 | int i1,j,j1,j2,k=0,k1,k2; + | ^~ +loki_init.c: In function 'InitValues': +loki_init.c:125:38: warning: this statement may fall through [-Wimplicit-fallthrough=] + 125 | tau_beta[mod]*=residual_var[mod]; + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +loki_init.c:126:18: note: here + 126 | case 1: + | ^~~~ loki_ibd.c: In function 'SetupIBD': loki_ibd.c:215:102: warning: format '%d' expects argument of type 'int', but argument 5 has type 'long unsigned int' [-Wformat=] 215 | fprintf(stderr,"Asked for 2*n_locations*n_pairs*sizeof(int)=2*%d*%d*%d=%d bytes\n",j,np,sizeof(int),2*j*np*sizeof(int)); @@ -601,46 +619,78 @@ | | | | int long unsigned int | %ld -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_trait_simple_peel.o loki_trait_simple_peel.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_trait_simple_sample.o loki_trait_simple_sample.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o get_par_probs.o get_par_probs.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o read_solar_idfile.o read_solar_idfile.c -gen_pen.c: In function 'calc_degree': -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o peel_to_par.o peel_to_par.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o update_segs.o update_segs.c -gen_pen.c:321:31: warning: variable 'k2' set but not used [-Wunused-but-set-variable] - 321 | int i1,j,j1,j2,k=0,k1,k2; - | ^~ loki_tlmoves.c: In function 'sample_mpos': loki_tlmoves.c:152:36: warning: variable 'idd' set but not used [-Wunused-but-set-variable] 152 | int i,j,locus,k2=-1,k3,ids,idd,sx,**seg,s,s1; | ^~~ -loki_init.c: In function 'InitValues': -loki_init.c:125:38: warning: this statement may fall through [-Wimplicit-fallthrough=] - 125 | tau_beta[mod]*=residual_var[mod]; - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -loki_init.c:126:18: note: here - 126 | case 1: - | ^~~~ -loki_output.c: In function 'OutputSample': +param_lex.c: In function 'yy_get_next_buffer': +param_lex.c:641:32: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] + 641 | for ( n = 0; n < max_size && \ + | ^ +param_lex.c:1161:17: note: in expansion of macro 'YY_INPUT' + 1161 | YY_INPUT( (&YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[number_to_move]), + | ^~~~~~~~ meiosis_scan.c: In function 'meiosis_scan': meiosis_scan.c:162:76: warning: variable 'n_comp1' set but not used [-Wunused-but-set-variable] 162 | int sex,kid,**seg,**seg1,kid1,nkids1,*kids1,lffg,symflag,n_qtl,qtl,n_comp1; | ^~~~~~~ +param_lex.c: At top level: +param_lex.c:1301:16: warning: 'input' defined but not used [-Wunused-function] + 1301 | static int input (void) + | ^~~~~ +param_lex.c:1260:17: warning: 'yyunput' defined but not used [-Wunused-function] + 1260 | static void yyunput (int c, register char * yy_bp ) + | ^~~~~~~ +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_identity.o loki_identity.c +param_lex.l: In function 'yylex': +param_lex.l:91:11: warning: 'strncpy' specified bound 512 equals destination size [-Wstringop-truncation] + 91 | (void)strncpy(linebuf,yytext+1,512); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +param_lex.l:64:11: warning: 'strncpy' specified bound 512 equals destination size [-Wstringop-truncation] + 64 | (void)strncpy(linebuf,yytext,512); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +loki_tlmoves.c:210:61: warning: 'x' may be used uninitialized [-Wmaybe-uninitialized] + 210 | r=.5*(1.0-exp(.02*(x-x1))); + | ~~^~~~ +loki_tlmoves.c:153:48: note: 'x' was declared here + 153 | double pp[2][50],ct1[2][50],ct2[2][50],x,x1,r,z,z1; + | ^ +loki_peel.c: In function 'peel_locus': +loki_peel.c:427:43: warning: 'z' may be used uninitialized [-Wmaybe-uninitialized] + 427 | if(z== -DBL_MAX) { + | ^ +loki_peel.c:145:26: note: 'z' was declared here + 145 | double like=0.0,like1,z,z1,theta,Mtp[2],Ptp[2],*pos,*eff,**count,*tpp,*freq1,*count1; + | ^ +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample_rand.o sample_rand.c +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample_effects.o sample_effects.c +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_setup.o loki_setup.c +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_dump.o loki_dump.c +loki_tlmoves.c: In function 'get_tl_position': +loki_tlmoves.c:623:17: warning: 'z' may be used uninitialized [-Wmaybe-uninitialized] + 623 | prior[i]+=z; + | ^~ +loki_tlmoves.c:606:16: note: 'z' was declared here + 606 | double z,z1,z2,map_length; + | ^ +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample_cens.o sample_cens.c +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o handle_res.o handle_res.c +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o print_data.o print_data.c +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o calc_var_locus.o calc_var_locus.c +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_output.o loki_output.c +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample_nu.o sample_nu.c +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_complex_peel.o loki_complex_peel.c +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_npl.o loki_npl.c +loki_output.c: In function 'OutputSample': loki_output.c:345:17: warning: this statement may fall through [-Wimplicit-fallthrough=] 345 | OutputSample_2(fptr,lp); | ^~~~~~~~~~~~~~~~~~~~~~~ loki_output.c:346:10: note: here 346 | case OUTPUT_VERSION_2_3: | ^~~~ +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_simple_sample.o loki_simple_sample.c +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_simple_peel.o loki_simple_peel.c loki_complex_peel.c: In function 'loki_complex_peelop': -loki_simple_sample.c: In function 'loki_simple_sample': -loki_simple_sample.c:25:58: warning: variable 'tpp2' set but not used [-Wunused-but-set-variable] - 25 | double *tp,p1,p2,z,z1,prob=0.0,pp[4],*tmp,*tpp1,*tpp2; - | ^~~~ -loki_simple_sample.c:25:52: warning: variable 'tpp1' set but not used [-Wunused-but-set-variable] - 25 | double *tp,p1,p2,z,z1,prob=0.0,pp[4],*tmp,*tpp1,*tpp2; - | ^~~~ loki_complex_peel.c:458:169: warning: format '%d' expects argument of type 'int', but argument 8 has type 'long unsigned int' [-Wformat=] 458 | (void)fprintf(stderr,"\nToo many individuals in output R-Function for marker %s\nn_peel = %d, n_all = %d, n_bits1 = %d, required size = %d, LONG_BIT = %d\n",marker[locus].name,n_peel,n_all,n_bits1,n_peel*n_bits1,LK_LONG_BIT); | ~^ @@ -650,33 +700,20 @@ loki_complex_peel.c:379:16: warning: variable 'max_terms' set but not used [-Wunused-but-set-variable] 379 | double max_terms,*tp,prob=0.0,z,p1,Konst=0.0; | ^~~~~~~~~ -loki_tlmoves.c:210:61: warning: 'x' may be used uninitialized [-Wmaybe-uninitialized] - 210 | r=.5*(1.0-exp(.02*(x-x1))); - | ~~^~~~ -loki_tlmoves.c:153:48: note: 'x' was declared here - 153 | double pp[2][50],ct1[2][50],ct2[2][50],x,x1,r,z,z1; - | ^ -param_lex.l: In function 'yylex': -param_lex.l:91:11: warning: 'strncpy' specified bound 512 equals destination size [-Wstringop-truncation] - 91 | (void)strncpy(linebuf,yytext+1,512); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -param_lex.l:64:11: warning: 'strncpy' specified bound 512 equals destination size [-Wstringop-truncation] - 64 | (void)strncpy(linebuf,yytext,512); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -loki_tlmoves.c: In function 'get_tl_position': -loki_tlmoves.c:623:17: warning: 'z' may be used uninitialized [-Wmaybe-uninitialized] - 623 | prior[i]+=z; - | ^~ -loki_tlmoves.c:606:16: note: 'z' was declared here - 606 | double z,z1,z2,map_length; - | ^ -loki_peel.c: In function 'peel_locus': -loki_peel.c:427:43: warning: 'z' may be used uninitialized [-Wmaybe-uninitialized] - 427 | if(z== -DBL_MAX) { - | ^ -loki_peel.c:145:26: note: 'z' was declared here - 145 | double like=0.0,like1,z,z1,theta,Mtp[2],Ptp[2],*pos,*eff,**count,*tpp,*freq1,*count1; - | ^ +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_trait_simple_peel.o loki_trait_simple_peel.c +loki_simple_sample.c: In function 'loki_simple_sample': +loki_simple_sample.c:25:58: warning: variable 'tpp2' set but not used [-Wunused-but-set-variable] + 25 | double *tp,p1,p2,z,z1,prob=0.0,pp[4],*tmp,*tpp1,*tpp2; + | ^~~~ +loki_simple_sample.c:25:52: warning: variable 'tpp1' set but not used [-Wunused-but-set-variable] + 25 | double *tp,p1,p2,z,z1,prob=0.0,pp[4],*tmp,*tpp1,*tpp2; + | ^~~~ +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_trait_simple_sample.o loki_trait_simple_sample.c +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o get_par_probs.o get_par_probs.c +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o read_solar_idfile.o read_solar_idfile.c +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o peel_to_par.o peel_to_par.c +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o update_segs.o update_segs.c +/usr/bin/ar cr libloki.a param_parse.o param_lex.o read_binfiles.o loki_utils.o kinship.o genedrop.o mat_utils.o output_recomb.o seg_pen.o gen_pen.o loki_ibd.o get_founders.o pass_founder_genes.o loki_simple_peel.c: In function 'loki_simple_peelop': loki_simple_peel.c:601:54: warning: 'cm[0]' may be used uninitialized [-Wmaybe-uninitialized] 601 | id_set2[i]=(cm[X_MAT]&a1)?lump[X_MAT]:i; @@ -690,6 +727,7 @@ loki_simple_peel.c:27:28: note: 'cm[1]' was declared here 27 | lk_ulong a,b,a1,b1,cm[2],*tmp_idx,*tmp_idx1,*cmm[2],mask; | ^~ +/usr/bin/ranlib libloki.a loki_simple_peel.c: In function 'loki_simple_peelop_x': loki_simple_peel.c:1279:54: warning: 'cm[0]' may be used uninitialized [-Wmaybe-uninitialized] 1279 | id_set2[i]=(cm[X_MAT]&a1)?lump[X_MAT]:i; @@ -703,8 +741,6 @@ loki_simple_peel.c:723:28: note: 'cm[1]' was declared here 723 | lk_ulong a,b,a1,b1,cm[2],*tmp_idx,*tmp_idx1,*cmm[2],mask; | ^~ -/usr/bin/ar cr libloki.a param_parse.o param_lex.o read_binfiles.o loki_utils.o kinship.o genedrop.o mat_utils.o output_recomb.o seg_pen.o gen_pen.o loki_ibd.o get_founders.o pass_founder_genes.o -/usr/bin/ranlib libloki.a gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -o loki loki.o loki_peel.o loki_init.o alloc_loki.o loki_sample.o loki_pen.o loki_tlmoves.o meiosis_scan.o loki_identity.o sample_rand.o sample_effects.o loki_setup.o loki_dump.o sample_cens.o handle_res.o print_data.o calc_var_locus.o loki_output.o sample_nu.o loki_complex_peel.o loki_npl.o loki_simple_sample.o loki_simple_peel.o loki_trait_simple_peel.o loki_trait_simple_sample.o get_par_probs.o read_solar_idfile.o peel_to_par.o update_segs.o -Wl,-z,relro -Wl,-z,now -L. -L../libsrc -lloki -lgen -lm make[2]: Leaving directory '/build/reproducible-path/loki-2.4.7.4/lokisrc' make[2]: Entering directory '/build/reproducible-path/loki-2.4.7.4/utils' @@ -737,7 +773,7 @@ debian/rules override_dh_auto_install-arch make[1]: Entering directory '/build/reproducible-path/loki-2.4.7.4' dh_auto_install -a - make -j42 install DESTDIR=/build/reproducible-path/loki-2.4.7.4/debian/tmp AM_UPDATE_INFO_DIR=no + make -j20 install DESTDIR=/build/reproducible-path/loki-2.4.7.4/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/loki-2.4.7.4' for subdir in libsrc prepsrc lokisrc utils; do \ (cd $subdir; make) \ @@ -856,8 +892,8 @@ dpkg-gencontrol: warning: package loki: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb -dpkg-deb: building package 'loki' in '../loki_2.4.7.4-12_amd64.deb'. dpkg-deb: building package 'loki-dbgsym' in '../loki-dbgsym_2.4.7.4-12_amd64.deb'. +dpkg-deb: building package 'loki' in '../loki_2.4.7.4-12_amd64.deb'. dpkg-deb: building package 'loki-doc' in '../loki-doc_2.4.7.4-12_all.deb'. dpkg-genbuildinfo --build=binary -O../loki_2.4.7.4-12_amd64.buildinfo dpkg-genchanges --build=binary -O../loki_2.4.7.4-12_amd64.changes @@ -866,12 +902,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3702951/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3702951/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/3459881 and its subdirectories -I: Current time: Wed Jan 21 18:24:16 -12 2026 -I: pbuilder-time-stamp: 1769063056 +I: removing directory /srv/workspace/pbuilder/3702951 and its subdirectories +I: Current time: Fri Dec 20 14:04:09 +14 2024 +I: pbuilder-time-stamp: 1734653049