Diff of the two buildlogs: -- --- b1/build.log 2025-09-04 01:16:39.074046665 +0000 +++ b2/build.log 2025-09-04 01:26:01.966716421 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Sep 3 13:14:39 -12 2025 -I: pbuilder-time-stamp: 1756948479 +I: Current time: Wed Oct 7 21:39:40 +14 2026 +I: pbuilder-time-stamp: 1791358780 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -33,53 +33,85 @@ dpkg-source: info: applying 0010-newer-GCC-support.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1063317/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1407575/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-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 Oct 7 07:40 /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/1407575/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1407575/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=40 ' - DISTRIBUTION='forky' - 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=42 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='d8da753e8a604b799069fe8984f18dbd' - 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='1063317' - PS1='# ' - PS2='> ' + INVOCATION_ID=a7c87ec97f064b0089ac1a3a1a8839ed + 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=1407575 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.xxHc5xK5/pbuilderrc_QVGj --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.xxHc5xK5/b1 --logfile b1/build.log bwa-mem2_2.2.1-1.dsc' - SUDO_GID='110' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.xxHc5xK5/pbuilderrc_1Usc --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.xxHc5xK5/b2 --logfile b2/build.log bwa-mem2_2.2.1-1.dsc' + SUDO_GID=110 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.12.41+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.41-1 (2025-08-12) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.41+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.41-1 (2025-08-12) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1063317/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1407575/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -154,7 +186,7 @@ Get: 31 http://deb.debian.org/debian forky/main amd64 help2man amd64 1.49.3 [198 kB] Get: 32 http://deb.debian.org/debian forky/main amd64 libsimde-dev all 0.8.2-3 [467 kB] Get: 33 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] -Fetched 12.8 MB in 0s (132 MB/s) +Fetched 12.8 MB in 0s (29.5 MB/s) Preconfiguring packages ... Selecting previously unselected package liblocale-gettext-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19897 files and directories currently installed.) @@ -301,7 +333,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/bwa-mem2-2.2.1/ && 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 > ../bwa-mem2_2.2.1-1_source.changes +I: user script /srv/workspace/pbuilder/1407575/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/1407575/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/bwa-mem2-2.2.1/ && 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 > ../bwa-mem2_2.2.1-1_source.changes dpkg-buildpackage: info: source package bwa-mem2 dpkg-buildpackage: info: source version 2.2.1-1 dpkg-buildpackage: info: source distribution unstable @@ -313,7 +349,7 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1' dh_auto_clean || true - make -j40 clean + make -j42 clean make[2]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1' rm -fr src/*.o libbwa.a bwa-mem2 bwa-mem2.sse41 bwa-mem2.sse42 bwa-mem2.avx bwa-mem2.avx2 bwa-mem2.avx512bw cd ext/safestringlib/ && make clean @@ -333,7 +369,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1' dh_auto_build -- EXE=bwa-mem2.sse2 ARCH_FLAGS='-msse2' - make -j40 "INSTALL=install --strip-program=true" EXE=bwa-mem2.sse2 ARCH_FLAGS=-msse2 + make -j42 "INSTALL=install --strip-program=true" EXE=bwa-mem2.sse2 ARCH_FLAGS=-msse2 make[2]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1' rm -f src/*.o libbwa.a; cd ext/safestringlib/ && make clean; make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' @@ -386,17 +422,6 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp_s.o safeclib/memcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcat_s.o safeclib/strcat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strnlen_s.o safeclib/strnlen_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy16_s.o safeclib/memcpy16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmpfld_s.o safeclib/strcmpfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strnterminate_s.o safeclib/strnterminate_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy32_s.o safeclib/memcpy32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmp_s.o safeclib/strcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strpbrk_s.o safeclib/strpbrk_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -In file included from src/kstring.cpp:28: -src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': -src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); - | ^~~~~~~~ In file included from src/utils.cpp:44: src/utils.cpp: In function 'pair64_t ks_ksmall_128(size_t, pair64_t*, size_t)': src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] @@ -408,6 +433,7 @@ src/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy16_s.o safeclib/memcpy16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ @@ -462,7 +488,6 @@ src/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy_s.o safeclib/memcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/utils.cpp: In function 'uint64_t ks_ksmall_64(size_t, uint64_t*, size_t)': src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } @@ -473,6 +498,7 @@ src/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmpfld_s.o safeclib/strcmpfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ @@ -527,18 +553,10 @@ src/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldin_s.o safeclib/strcpyfldin_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strprefix_s.o safeclib/strprefix_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove16_s.o safeclib/memmove16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldout_s.o safeclib/strcpyfldout_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strremovews_s.o safeclib/strremovews_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove32_s.o safeclib/memmove32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfld_s.o safeclib/strcpyfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strspn_s.o safeclib/strspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove_s.o safeclib/memmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpy_s.o safeclib/strcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strstr_s.o safeclib/strstr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/mem_primitives_lib.o safeclib/mem_primitives_lib.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strnterminate_s.o safeclib/strnterminate_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy32_s.o safeclib/memcpy32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmp_s.o safeclib/strcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strpbrk_s.o safeclib/strpbrk_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/utils.cpp: In function 'int ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)': src/kseq.h:135:109: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 135 | memcpy_bwamem(str->s + str->l, str->m - str->l, ks->buf + ks->begin, i - ks->begin, __FILE__, __LINE__); \ @@ -552,14 +570,28 @@ src/utils.cpp:50:1: note: in expansion of macro 'KSEQ_INIT2' 50 | KSEQ_INIT2(, gzFile, err_gzread) | ^~~~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy_s.o safeclib/memcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldin_s.o safeclib/strcpyfldin_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +In file included from src/kstring.cpp:28: +src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': +src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); + | ^~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strprefix_s.o safeclib/strprefix_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove16_s.o safeclib/memmove16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldout_s.o safeclib/strcpyfldout_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strremovews_s.o safeclib/strremovews_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove32_s.o safeclib/memmove32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfld_s.o safeclib/strcpyfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strspn_s.o safeclib/strspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove_s.o safeclib/memmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpy_s.o safeclib/strcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strstr_s.o safeclib/strstr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/mem_primitives_lib.o safeclib/mem_primitives_lib.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcspn_s.o safeclib/strcspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtok_s.o safeclib/strtok_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstchar_s.o safeclib/strfirstchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtolowercase_s.o safeclib/strtolowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -src/kopen.cpp: In function 'int ftp_open(const char*)': -src/kopen.cpp:257:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 257 | memcpy_bwamem(pasv_ip, 4 * sizeof(int), v, 4 * sizeof(int), __FILE__, __LINE__); - | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset16_s.o safeclib/memset16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstdiff_s.o safeclib/strfirstdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtouppercase_s.o safeclib/strtouppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -572,6 +604,10 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero16_s.o safeclib/memzero16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisascii_s.o safeclib/strisascii_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcscat_s.o safeclib/wcscat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +src/kopen.cpp: In function 'int ftp_open(const char*)': +src/kopen.cpp:257:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 257 | memcpy_bwamem(pasv_ip, 4 * sizeof(int), v, 4 * sizeof(int), __FILE__, __LINE__); + | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero32_s.o safeclib/memzero32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisdigit_s.o safeclib/strisdigit_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcscpy_s.o safeclib/wcscpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -609,22 +645,22 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +ar rcs libsafestring.a obj/abort_handler_s.o obj/stpcpy_s.o obj/strlastsame_s.o obj/ignore_handler_s.o obj/stpncpy_s.o obj/strljustify_s.o obj/memcmp16_s.o obj/strcasecmp_s.o obj/strncat_s.o obj/memcmp32_s.o obj/strcasestr_s.o obj/strncpy_s.o obj/memcmp_s.o obj/strcat_s.o obj/strnlen_s.o obj/memcpy16_s.o obj/strcmpfld_s.o obj/strnterminate_s.o obj/memcpy32_s.o obj/strcmp_s.o obj/strpbrk_s.o obj/memcpy_s.o obj/strcpyfldin_s.o obj/strprefix_s.o obj/memmove16_s.o obj/strcpyfldout_s.o obj/strremovews_s.o obj/memmove32_s.o obj/strcpyfld_s.o obj/strspn_s.o obj/memmove_s.o obj/strcpy_s.o obj/strstr_s.o obj/mem_primitives_lib.o obj/strcspn_s.o obj/strtok_s.o obj/strfirstchar_s.o obj/strtolowercase_s.o obj/memset16_s.o obj/strfirstdiff_s.o obj/strtouppercase_s.o obj/memset32_s.o obj/strfirstsame_s.o obj/strzero_s.o obj/memset_s.o obj/strisalphanumeric_s.o obj/wcpcpy_s.o obj/memzero16_s.o obj/strisascii_s.o obj/wcscat_s.o obj/memzero32_s.o obj/strisdigit_s.o obj/wcscpy_s.o obj/memzero_s.o obj/strishex_s.o obj/wcsncat_s.o obj/strislowercase_s.o obj/wcsncpy_s.o obj/safe_mem_constraint.o obj/strismixedcase_s.o obj/wcsnlen_s.o obj/strispassword_s.o obj/wmemcmp_s.o obj/safe_str_constraint.o obj/strisuppercase_s.o obj/wmemcpy_s.o obj/strlastchar_s.o obj/wmemmove_s.o obj/snprintf_support.o obj/strlastdiff_s.o obj/wmemset_s.o +make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' In file included from src/bwa.cpp:39: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ -ar rcs libsafestring.a obj/abort_handler_s.o obj/stpcpy_s.o obj/strlastsame_s.o obj/ignore_handler_s.o obj/stpncpy_s.o obj/strljustify_s.o obj/memcmp16_s.o obj/strcasecmp_s.o obj/strncat_s.o obj/memcmp32_s.o obj/strcasestr_s.o obj/strncpy_s.o obj/memcmp_s.o obj/strcat_s.o obj/strnlen_s.o obj/memcpy16_s.o obj/strcmpfld_s.o obj/strnterminate_s.o obj/memcpy32_s.o obj/strcmp_s.o obj/strpbrk_s.o obj/memcpy_s.o obj/strcpyfldin_s.o obj/strprefix_s.o obj/memmove16_s.o obj/strcpyfldout_s.o obj/strremovews_s.o obj/memmove32_s.o obj/strcpyfld_s.o obj/strspn_s.o obj/memmove_s.o obj/strcpy_s.o obj/strstr_s.o obj/mem_primitives_lib.o obj/strcspn_s.o obj/strtok_s.o obj/strfirstchar_s.o obj/strtolowercase_s.o obj/memset16_s.o obj/strfirstdiff_s.o obj/strtouppercase_s.o obj/memset32_s.o obj/strfirstsame_s.o obj/strzero_s.o obj/memset_s.o obj/strisalphanumeric_s.o obj/wcpcpy_s.o obj/memzero16_s.o obj/strisascii_s.o obj/wcscat_s.o obj/memzero32_s.o obj/strisdigit_s.o obj/wcscpy_s.o obj/memzero_s.o obj/strishex_s.o obj/wcsncat_s.o obj/strislowercase_s.o obj/wcsncpy_s.o obj/safe_mem_constraint.o obj/strismixedcase_s.o obj/wcsnlen_s.o obj/strispassword_s.o obj/wmemcmp_s.o obj/safe_str_constraint.o obj/strisuppercase_s.o obj/wmemcpy_s.o obj/strlastchar_s.o obj/wmemmove_s.o obj/snprintf_support.o obj/strlastdiff_s.o obj/wmemset_s.o -make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' In file included from src/bwamem.h:47, - from src/bwamem_extra.cpp:33: + from src/kthread.h:37, + from src/kthread.cpp:32: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ In file included from src/bwamem.h:47, - from src/kthread.h:37, - from src/kthread.cpp:32: + from src/bwamem_extra.cpp:33: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); @@ -634,6 +670,19 @@ src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ +In file included from src/bwamem.h:47, + from src/fastmap.h:45, + from src/fastmap.cpp:42: +src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': +src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); + | ^~~~~~~~ +In file included from src/main.h:36, + from src/main.cpp:35: +src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': +src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); + | ^~~~~~~~ src/bwamem_pair.cpp: In function 'int mem_matesw_batch_pre(const mem_opt_t*, const bntseq_t*, const uint8_t*, const mem_pestat_t*, const mem_alnreg_t*, int, const uint8_t*, mem_alnreg_v*, mem_cache*, int, int32_t, int32_t&, int32_t&, int32_t)': src/bwamem_pair.cpp:1028:33: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 1028 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufRefs in %s\n", @@ -644,12 +693,6 @@ src/bwamem_pair.cpp:1062:33: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 1062 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairs in %s\n", tid, __func__); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from src/main.h:36, - from src/main.cpp:35: -src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': -src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); - | ^~~~~~~~ In file included from src/bwamem.h:47, from src/bwamem.cpp:34: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': @@ -663,13 +706,6 @@ | | | | int int64_t {aka long int} | %ld -In file included from src/bwamem.h:47, - from src/fastmap.h:45, - from src/fastmap.cpp:42: -src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': -src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); - | ^~~~~~~~ In file included from src/bwamem.h:50: src/bwamem.cpp: In function 'bwtintv_t ks_ksmall_mem_intv(size_t, bwtintv_t*, size_t)': src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] @@ -1233,6 +1269,11 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/stpncpy_s.o safeclib/stpncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strljustify_s.o safeclib/strljustify_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp16_s.o safeclib/memcmp16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +In file included from src/kstring.cpp:28: +src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': +src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); + | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcasecmp_s.o safeclib/strcasecmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strncat_s.o safeclib/strncat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp32_s.o safeclib/memcmp32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -1247,11 +1288,26 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy32_s.o safeclib/memcpy32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmp_s.o safeclib/strcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strpbrk_s.o safeclib/strpbrk_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -In file included from src/kstring.cpp:28: -src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': -src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); - | ^~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy_s.o safeclib/memcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldin_s.o safeclib/strcpyfldin_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strprefix_s.o safeclib/strprefix_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove16_s.o safeclib/memmove16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldout_s.o safeclib/strcpyfldout_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strremovews_s.o safeclib/strremovews_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +src/kopen.cpp: In function 'int ftp_open(const char*)': +src/kopen.cpp:257:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 257 | memcpy_bwamem(pasv_ip, 4 * sizeof(int), v, 4 * sizeof(int), __FILE__, __LINE__); + | ^~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove32_s.o safeclib/memmove32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfld_s.o safeclib/strcpyfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strspn_s.o safeclib/strspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove_s.o safeclib/memmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpy_s.o safeclib/strcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strstr_s.o safeclib/strstr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/mem_primitives_lib.o safeclib/mem_primitives_lib.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcspn_s.o safeclib/strcspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtok_s.o safeclib/strtok_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstchar_s.o safeclib/strfirstchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS In file included from src/utils.cpp:44: src/utils.cpp: In function 'pair64_t ks_ksmall_128(size_t, pair64_t*, size_t)': src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] @@ -1299,6 +1355,7 @@ src/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtolowercase_s.o safeclib/strtolowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ @@ -1308,6 +1365,8 @@ src/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset16_s.o safeclib/memset16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstdiff_s.o safeclib/strfirstdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ @@ -1317,6 +1376,9 @@ src/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtouppercase_s.o safeclib/strtouppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset32_s.o safeclib/memset32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstsame_s.o safeclib/strfirstsame_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/utils.cpp: In function 'uint64_t ks_ksmall_64(size_t, uint64_t*, size_t)': src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } @@ -1363,6 +1425,8 @@ src/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strzero_s.o safeclib/strzero_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset_s.o safeclib/memset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ @@ -1381,10 +1445,13 @@ src/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ -src/kopen.cpp: In function 'int ftp_open(const char*)': -src/kopen.cpp:257:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 257 | memcpy_bwamem(pasv_ip, 4 * sizeof(int), v, 4 * sizeof(int), __FILE__, __LINE__); - | ^~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisalphanumeric_s.o safeclib/strisalphanumeric_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcpcpy_s.o safeclib/wcpcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero16_s.o safeclib/memzero16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisascii_s.o safeclib/strisascii_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcscat_s.o safeclib/wcscat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero32_s.o safeclib/memzero32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisdigit_s.o safeclib/strisdigit_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/utils.cpp: In function 'int ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)': src/kseq.h:135:109: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 135 | memcpy_bwamem(str->s + str->l, str->m - str->l, ks->buf + ks->begin, i - ks->begin, __FILE__, __LINE__); \ @@ -1398,10 +1465,25 @@ src/utils.cpp:50:1: note: in expansion of macro 'KSEQ_INIT2' 50 | KSEQ_INIT2(, gzFile, err_gzread) | ^~~~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy_s.o safeclib/memcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldin_s.o safeclib/strcpyfldin_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strprefix_s.o safeclib/strprefix_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove16_s.o safeclib/memmove16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcscpy_s.o safeclib/wcscpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero_s.o safeclib/memzero_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strishex_s.o safeclib/strishex_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsncat_s.o safeclib/wcsncat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strislowercase_s.o safeclib/strislowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsncpy_s.o safeclib/wcsncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/safe_mem_constraint.o safeclib/safe_mem_constraint.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strismixedcase_s.o safeclib/strismixedcase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsnlen_s.o safeclib/wcsnlen_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strispassword_s.o safeclib/strispassword_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemcmp_s.o safeclib/wmemcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/safe_str_constraint.o safeclib/safe_str_constraint.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisuppercase_s.o safeclib/strisuppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemcpy_s.o safeclib/wmemcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastchar_s.o safeclib/strlastchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemmove_s.o safeclib/wmemmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/snprintf_support.o safeclib/snprintf_support.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastdiff_s.o safeclib/strlastdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemset_s.o safeclib/wmemset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/kopen.cpp: In function 'void* kopen(const char*, int*)': src/kopen.cpp:262:27: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 262 | sprintf(port2, "%d", pasv_port); @@ -1423,51 +1505,32 @@ src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldout_s.o safeclib/strcpyfldout_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strremovews_s.o safeclib/strremovews_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove32_s.o safeclib/memmove32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfld_s.o safeclib/strcpyfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strspn_s.o safeclib/strspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove_s.o safeclib/memmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpy_s.o safeclib/strcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strstr_s.o safeclib/strstr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/mem_primitives_lib.o safeclib/mem_primitives_lib.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcspn_s.o safeclib/strcspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtok_s.o safeclib/strtok_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstchar_s.o safeclib/strfirstchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtolowercase_s.o safeclib/strtolowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset16_s.o safeclib/memset16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstdiff_s.o safeclib/strfirstdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtouppercase_s.o safeclib/strtouppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +ar rcs libsafestring.a obj/abort_handler_s.o obj/stpcpy_s.o obj/strlastsame_s.o obj/ignore_handler_s.o obj/stpncpy_s.o obj/strljustify_s.o obj/memcmp16_s.o obj/strcasecmp_s.o obj/strncat_s.o obj/memcmp32_s.o obj/strcasestr_s.o obj/strncpy_s.o obj/memcmp_s.o obj/strcat_s.o obj/strnlen_s.o obj/memcpy16_s.o obj/strcmpfld_s.o obj/strnterminate_s.o obj/memcpy32_s.o obj/strcmp_s.o obj/strpbrk_s.o obj/memcpy_s.o obj/strcpyfldin_s.o obj/strprefix_s.o obj/memmove16_s.o obj/strcpyfldout_s.o obj/strremovews_s.o obj/memmove32_s.o obj/strcpyfld_s.o obj/strspn_s.o obj/memmove_s.o obj/strcpy_s.o obj/strstr_s.o obj/mem_primitives_lib.o obj/strcspn_s.o obj/strtok_s.o obj/strfirstchar_s.o obj/strtolowercase_s.o obj/memset16_s.o obj/strfirstdiff_s.o obj/strtouppercase_s.o obj/memset32_s.o obj/strfirstsame_s.o obj/strzero_s.o obj/memset_s.o obj/strisalphanumeric_s.o obj/wcpcpy_s.o obj/memzero16_s.o obj/strisascii_s.o obj/wcscat_s.o obj/memzero32_s.o obj/strisdigit_s.o obj/wcscpy_s.o obj/memzero_s.o obj/strishex_s.o obj/wcsncat_s.o obj/strislowercase_s.o obj/wcsncpy_s.o obj/safe_mem_constraint.o obj/strismixedcase_s.o obj/wcsnlen_s.o obj/strispassword_s.o obj/wmemcmp_s.o obj/safe_str_constraint.o obj/strisuppercase_s.o obj/wmemcpy_s.o obj/strlastchar_s.o obj/wmemmove_s.o obj/snprintf_support.o obj/strlastdiff_s.o obj/wmemset_s.o +make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' +In file included from src/bwamem.h:47, + from src/kthread.h:37, + from src/kthread.cpp:32: +src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': +src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); + | ^~~~~~~~ In file included from src/bwamem.h:47, from src/bwamem_extra.cpp:33: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset32_s.o safeclib/memset32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstsame_s.o safeclib/strfirstsame_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strzero_s.o safeclib/strzero_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset_s.o safeclib/memset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisalphanumeric_s.o safeclib/strisalphanumeric_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS In file included from src/bwamem_pair.cpp:36: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ -In file included from src/bwamem.h:47, - from src/kthread.h:37, - from src/kthread.cpp:32: +In file included from src/main.h:36, + from src/main.cpp:35: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcpcpy_s.o safeclib/wcpcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero16_s.o safeclib/memzero16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisascii_s.o safeclib/strisascii_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcscat_s.o safeclib/wcscat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero32_s.o safeclib/memzero32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisdigit_s.o safeclib/strisdigit_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/bwamem_pair.cpp: In function 'int mem_matesw_batch_pre(const mem_opt_t*, const bntseq_t*, const uint8_t*, const mem_pestat_t*, const mem_alnreg_t*, int, const uint8_t*, mem_alnreg_v*, mem_cache*, int, int32_t, int32_t&, int32_t&, int32_t)': src/bwamem_pair.cpp:1028:33: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 1028 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufRefs in %s\n", @@ -1478,45 +1541,12 @@ src/bwamem_pair.cpp:1062:33: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 1062 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairs in %s\n", tid, __func__); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcscpy_s.o safeclib/wcscpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero_s.o safeclib/memzero_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strishex_s.o safeclib/strishex_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsncat_s.o safeclib/wcsncat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strislowercase_s.o safeclib/strislowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsncpy_s.o safeclib/wcsncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/safe_mem_constraint.o safeclib/safe_mem_constraint.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strismixedcase_s.o safeclib/strismixedcase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsnlen_s.o safeclib/wcsnlen_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strispassword_s.o safeclib/strispassword_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemcmp_s.o safeclib/wmemcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/safe_str_constraint.o safeclib/safe_str_constraint.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisuppercase_s.o safeclib/strisuppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemcpy_s.o safeclib/wmemcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastchar_s.o safeclib/strlastchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemmove_s.o safeclib/wmemmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/snprintf_support.o safeclib/snprintf_support.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastdiff_s.o safeclib/strlastdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemset_s.o safeclib/wmemset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -ar rcs libsafestring.a obj/abort_handler_s.o obj/stpcpy_s.o obj/strlastsame_s.o obj/ignore_handler_s.o obj/stpncpy_s.o obj/strljustify_s.o obj/memcmp16_s.o obj/strcasecmp_s.o obj/strncat_s.o obj/memcmp32_s.o obj/strcasestr_s.o obj/strncpy_s.o obj/memcmp_s.o obj/strcat_s.o obj/strnlen_s.o obj/memcpy16_s.o obj/strcmpfld_s.o obj/strnterminate_s.o obj/memcpy32_s.o obj/strcmp_s.o obj/strpbrk_s.o obj/memcpy_s.o obj/strcpyfldin_s.o obj/strprefix_s.o obj/memmove16_s.o obj/strcpyfldout_s.o obj/strremovews_s.o obj/memmove32_s.o obj/strcpyfld_s.o obj/strspn_s.o obj/memmove_s.o obj/strcpy_s.o obj/strstr_s.o obj/mem_primitives_lib.o obj/strcspn_s.o obj/strtok_s.o obj/strfirstchar_s.o obj/strtolowercase_s.o obj/memset16_s.o obj/strfirstdiff_s.o obj/strtouppercase_s.o obj/memset32_s.o obj/strfirstsame_s.o obj/strzero_s.o obj/memset_s.o obj/strisalphanumeric_s.o obj/wcpcpy_s.o obj/memzero16_s.o obj/strisascii_s.o obj/wcscat_s.o obj/memzero32_s.o obj/strisdigit_s.o obj/wcscpy_s.o obj/memzero_s.o obj/strishex_s.o obj/wcsncat_s.o obj/strislowercase_s.o obj/wcsncpy_s.o obj/safe_mem_constraint.o obj/strismixedcase_s.o obj/wcsnlen_s.o obj/strispassword_s.o obj/wmemcmp_s.o obj/safe_str_constraint.o obj/strisuppercase_s.o obj/wmemcpy_s.o obj/strlastchar_s.o obj/wmemmove_s.o obj/snprintf_support.o obj/strlastdiff_s.o obj/wmemset_s.o -In file included from src/main.h:36, - from src/main.cpp:35: -src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': -src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); - | ^~~~~~~~ In file included from src/bwamem.h:47, from src/bwamem.cpp:34: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ -In file included from src/bwamem.h:47, - from src/fastmap.h:45, - from src/fastmap.cpp:42: -src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': -src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); - | ^~~~~~~~ In file included from src/bwamem.h:50: src/bwamem.cpp: In function 'bwtintv_t ks_ksmall_mem_intv(size_t, bwtintv_t*, size_t)': src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] @@ -1646,13 +1676,6 @@ src/bwamem.cpp:49:1: note: in expansion of macro 'KSORT_INIT' 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ -src/FMI_search.cpp: In member function 'int FMI_search::build_fm_index(const char*, char*, int64_t, int64_t*, int64_t*)': -src/FMI_search.cpp:278:28: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=] - 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); - | ~^ ~~~ - | | | - | int int64_t {aka long int} - | %ld src/bwamem.cpp: In function 'mem_chain_t ks_ksmall_mem_flt(size_t, mem_chain_t*, size_t)': src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } @@ -1781,7 +1804,6 @@ src/bwamem.cpp:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' src/bwamem.cpp: In function 'mem_alnreg_t ks_ksmall_mem_ars(size_t, mem_alnreg_t*, size_t)': src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } @@ -2043,6 +2065,20 @@ src/bwamem.cpp:2374:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2374 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +src/FMI_search.cpp: In member function 'int FMI_search::build_fm_index(const char*, char*, int64_t, int64_t*, int64_t*)': +src/FMI_search.cpp:278:28: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=] + 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); + | ~^ ~~~ + | | | + | int int64_t {aka long int} + | %ld +In file included from src/bwamem.h:47, + from src/fastmap.h:45, + from src/fastmap.cpp:42: +src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': +src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); + | ^~~~~~~~ ar rcs libbwa.a src/fastmap.o src/bwtindex.o src/utils.o src/memcpy_bwamem.o src/kthread.o src/kstring.o src/ksw.o src/bntseq.o src/bwamem.o src/profiling.o src/bandedSWA.o src/FMI_search.o src/read_index_ele.o src/bwamem_pair.o src/kswv.o src/bwa.o src/bwamem_extra.o src/kopen.o g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now src/main.o libbwa.a -lpthread -lm -lz -L. -lbwa -Lext/safestringlib -lsafestring -o bwa-mem2.sse42 make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1' @@ -2102,13 +2138,19 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy32_s.o safeclib/memcpy32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmp_s.o safeclib/strcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strpbrk_s.o safeclib/strpbrk_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy_s.o safeclib/memcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldin_s.o safeclib/strcpyfldin_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS In file included from src/kstring.cpp:28: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy_s.o safeclib/memcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldin_s.o safeclib/strcpyfldin_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strprefix_s.o safeclib/strprefix_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove16_s.o safeclib/memmove16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldout_s.o safeclib/strcpyfldout_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strremovews_s.o safeclib/strremovews_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove32_s.o safeclib/memmove32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfld_s.o safeclib/strcpyfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS In file included from src/utils.cpp:44: src/utils.cpp: In function 'pair64_t ks_ksmall_128(size_t, pair64_t*, size_t)': src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] @@ -2174,6 +2216,7 @@ src/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strspn_s.o safeclib/strspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/utils.cpp: In function 'uint64_t ks_ksmall_64(size_t, uint64_t*, size_t)': src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } @@ -2238,47 +2281,11 @@ src/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strprefix_s.o safeclib/strprefix_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove16_s.o safeclib/memmove16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldout_s.o safeclib/strcpyfldout_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strremovews_s.o safeclib/strremovews_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove32_s.o safeclib/memmove32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfld_s.o safeclib/strcpyfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -src/utils.cpp: In function 'int ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)': -src/kseq.h:135:109: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 135 | memcpy_bwamem(str->s + str->l, str->m - str->l, ks->buf + ks->begin, i - ks->begin, __FILE__, __LINE__); \ - | ^~~~~~~~ -src/kseq.h:159:9: note: in expansion of macro '__KS_GETUNTIL' - 159 | __KS_GETUNTIL(__read, __bufsize) - | ^~~~~~~~~~~~~ -src/kseq.h:237:9: note: in expansion of macro 'KSTREAM_INIT' - 237 | KSTREAM_INIT(type_t, __read, 16384) \ - | ^~~~~~~~~~~~ -src/utils.cpp:50:1: note: in expansion of macro 'KSEQ_INIT2' - 50 | KSEQ_INIT2(, gzFile, err_gzread) - | ^~~~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove_s.o safeclib/memmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/kopen.cpp: In function 'int ftp_open(const char*)': src/kopen.cpp:257:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 257 | memcpy_bwamem(pasv_ip, 4 * sizeof(int), v, 4 * sizeof(int), __FILE__, __LINE__); | ^~~~~~~~ -src/kopen.cpp: In function 'void* kopen(const char*, int*)': -src/kopen.cpp:262:27: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] - 262 | sprintf(port2, "%d", pasv_port); - | ^ -In file included from /usr/include/stdio.h:970, - from src/kopen.cpp:30: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'int ftp_open(const char*)' at src/kopen.cpp:262:9, - inlined from 'void* kopen(const char*, int*)' at src/kopen.cpp:325:21: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 10 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strspn_s.o safeclib/strspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove_s.o safeclib/memmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpy_s.o safeclib/strcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strstr_s.o safeclib/strstr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/mem_primitives_lib.o safeclib/mem_primitives_lib.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -2291,6 +2298,19 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtouppercase_s.o safeclib/strtouppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset32_s.o safeclib/memset32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstsame_s.o safeclib/strfirstsame_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +src/utils.cpp: In function 'int ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)': +src/kseq.h:135:109: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 135 | memcpy_bwamem(str->s + str->l, str->m - str->l, ks->buf + ks->begin, i - ks->begin, __FILE__, __LINE__); \ + | ^~~~~~~~ +src/kseq.h:159:9: note: in expansion of macro '__KS_GETUNTIL' + 159 | __KS_GETUNTIL(__read, __bufsize) + | ^~~~~~~~~~~~~ +src/kseq.h:237:9: note: in expansion of macro 'KSTREAM_INIT' + 237 | KSTREAM_INIT(type_t, __read, 16384) \ + | ^~~~~~~~~~~~ +src/utils.cpp:50:1: note: in expansion of macro 'KSEQ_INIT2' + 50 | KSEQ_INIT2(, gzFile, err_gzread) + | ^~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strzero_s.o safeclib/strzero_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset_s.o safeclib/memset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisalphanumeric_s.o safeclib/strisalphanumeric_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -2319,6 +2339,22 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/snprintf_support.o safeclib/snprintf_support.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastdiff_s.o safeclib/strlastdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemset_s.o safeclib/wmemset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +src/kopen.cpp: In function 'void* kopen(const char*, int*)': +src/kopen.cpp:262:27: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] + 262 | sprintf(port2, "%d", pasv_port); + | ^ +In file included from /usr/include/stdio.h:970, + from src/kopen.cpp:30: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'int ftp_open(const char*)' at src/kopen.cpp:262:9, + inlined from 'void* kopen(const char*, int*)' at src/kopen.cpp:325:21: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 10 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ In file included from src/bwa.cpp:39: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] @@ -2326,20 +2362,20 @@ | ^~~~~~~~ ar rcs libsafestring.a obj/abort_handler_s.o obj/stpcpy_s.o obj/strlastsame_s.o obj/ignore_handler_s.o obj/stpncpy_s.o obj/strljustify_s.o obj/memcmp16_s.o obj/strcasecmp_s.o obj/strncat_s.o obj/memcmp32_s.o obj/strcasestr_s.o obj/strncpy_s.o obj/memcmp_s.o obj/strcat_s.o obj/strnlen_s.o obj/memcpy16_s.o obj/strcmpfld_s.o obj/strnterminate_s.o obj/memcpy32_s.o obj/strcmp_s.o obj/strpbrk_s.o obj/memcpy_s.o obj/strcpyfldin_s.o obj/strprefix_s.o obj/memmove16_s.o obj/strcpyfldout_s.o obj/strremovews_s.o obj/memmove32_s.o obj/strcpyfld_s.o obj/strspn_s.o obj/memmove_s.o obj/strcpy_s.o obj/strstr_s.o obj/mem_primitives_lib.o obj/strcspn_s.o obj/strtok_s.o obj/strfirstchar_s.o obj/strtolowercase_s.o obj/memset16_s.o obj/strfirstdiff_s.o obj/strtouppercase_s.o obj/memset32_s.o obj/strfirstsame_s.o obj/strzero_s.o obj/memset_s.o obj/strisalphanumeric_s.o obj/wcpcpy_s.o obj/memzero16_s.o obj/strisascii_s.o obj/wcscat_s.o obj/memzero32_s.o obj/strisdigit_s.o obj/wcscpy_s.o obj/memzero_s.o obj/strishex_s.o obj/wcsncat_s.o obj/strislowercase_s.o obj/wcsncpy_s.o obj/safe_mem_constraint.o obj/strismixedcase_s.o obj/wcsnlen_s.o obj/strispassword_s.o obj/wmemcmp_s.o obj/safe_str_constraint.o obj/strisuppercase_s.o obj/wmemcpy_s.o obj/strlastchar_s.o obj/wmemmove_s.o obj/snprintf_support.o obj/strlastdiff_s.o obj/wmemset_s.o make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' -In file included from src/bwamem_pair.cpp:36: +In file included from src/bwamem.h:47, + from src/kthread.h:37, + from src/kthread.cpp:32: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ -In file included from src/bwamem.h:47, - from src/bwamem_extra.cpp:33: +In file included from src/bwamem_pair.cpp:36: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ In file included from src/bwamem.h:47, - from src/kthread.h:37, - from src/kthread.cpp:32: + from src/bwamem_extra.cpp:33: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); @@ -2366,20 +2402,6 @@ src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ -src/FMI_search.cpp: In member function 'int FMI_search::build_fm_index(const char*, char*, int64_t, int64_t*, int64_t*)': -src/FMI_search.cpp:278:28: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=] - 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); - | ~^ ~~~ - | | | - | int int64_t {aka long int} - | %ld -In file included from src/bwamem.h:47, - from src/fastmap.h:45, - from src/fastmap.cpp:42: -src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': -src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); - | ^~~~~~~~ In file included from src/bwamem.h:50: src/bwamem.cpp: In function 'bwtintv_t ks_ksmall_mem_intv(size_t, bwtintv_t*, size_t)': src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] @@ -2898,6 +2920,20 @@ src/bwamem.cpp:2374:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2374 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from src/bwamem.h:47, + from src/fastmap.h:45, + from src/fastmap.cpp:42: +src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': +src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); + | ^~~~~~~~ +src/FMI_search.cpp: In member function 'int FMI_search::build_fm_index(const char*, char*, int64_t, int64_t*, int64_t*)': +src/FMI_search.cpp:278:28: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=] + 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); + | ~^ ~~~ + | | | + | int int64_t {aka long int} + | %ld ar rcs libbwa.a src/fastmap.o src/bwtindex.o src/utils.o src/memcpy_bwamem.o src/kthread.o src/kstring.o src/ksw.o src/bntseq.o src/bwamem.o src/profiling.o src/bandedSWA.o src/FMI_search.o src/read_index_ele.o src/bwamem_pair.o src/kswv.o src/bwa.o src/bwamem_extra.o src/kopen.o g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now src/main.o libbwa.a -lpthread -lm -lz -L. -lbwa -Lext/safestringlib -lsafestring -o bwa-mem2.avx make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1' @@ -2939,26 +2975,6 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/abort_handler_s.o safeclib/abort_handler_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/stpcpy_s.o safeclib/stpcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastsame_s.o safeclib/strlastsame_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/ignore_handler_s.o safeclib/ignore_handler_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/stpncpy_s.o safeclib/stpncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strljustify_s.o safeclib/strljustify_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp16_s.o safeclib/memcmp16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcasecmp_s.o safeclib/strcasecmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strncat_s.o safeclib/strncat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp32_s.o safeclib/memcmp32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcasestr_s.o safeclib/strcasestr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strncpy_s.o safeclib/strncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp_s.o safeclib/memcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcat_s.o safeclib/strcat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strnlen_s.o safeclib/strnlen_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy16_s.o safeclib/memcpy16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmpfld_s.o safeclib/strcmpfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strnterminate_s.o safeclib/strnterminate_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy32_s.o safeclib/memcpy32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmp_s.o safeclib/strcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strpbrk_s.o safeclib/strpbrk_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy_s.o safeclib/memcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldin_s.o safeclib/strcpyfldin_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS In file included from src/utils.cpp:44: src/utils.cpp: In function 'pair64_t ks_ksmall_128(size_t, pair64_t*, size_t)': src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] @@ -2970,6 +2986,7 @@ src/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/ignore_handler_s.o safeclib/ignore_handler_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ @@ -2997,6 +3014,7 @@ src/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/stpncpy_s.o safeclib/stpncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ @@ -3024,7 +3042,6 @@ src/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strprefix_s.o safeclib/strprefix_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/utils.cpp: In function 'uint64_t ks_ksmall_64(size_t, uint64_t*, size_t)': src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } @@ -3089,21 +3106,14 @@ src/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove16_s.o safeclib/memmove16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldout_s.o safeclib/strcpyfldout_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strremovews_s.o safeclib/strremovews_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove32_s.o safeclib/memmove32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -In file included from src/kstring.cpp:28: -src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': -src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); - | ^~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfld_s.o safeclib/strcpyfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strspn_s.o safeclib/strspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove_s.o safeclib/memmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpy_s.o safeclib/strcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strstr_s.o safeclib/strstr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/mem_primitives_lib.o safeclib/mem_primitives_lib.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strljustify_s.o safeclib/strljustify_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp16_s.o safeclib/memcmp16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcasecmp_s.o safeclib/strcasecmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strncat_s.o safeclib/strncat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp32_s.o safeclib/memcmp32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcasestr_s.o safeclib/strcasestr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strncpy_s.o safeclib/strncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp_s.o safeclib/memcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/utils.cpp: In function 'int ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)': src/kseq.h:135:109: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 135 | memcpy_bwamem(str->s + str->l, str->m - str->l, ks->buf + ks->begin, i - ks->begin, __FILE__, __LINE__); \ @@ -3117,13 +3127,39 @@ src/utils.cpp:50:1: note: in expansion of macro 'KSEQ_INIT2' 50 | KSEQ_INIT2(, gzFile, err_gzread) | ^~~~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcspn_s.o safeclib/strcspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtok_s.o safeclib/strtok_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstchar_s.o safeclib/strfirstchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcat_s.o safeclib/strcat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strnlen_s.o safeclib/strnlen_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy16_s.o safeclib/memcpy16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmpfld_s.o safeclib/strcmpfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strnterminate_s.o safeclib/strnterminate_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy32_s.o safeclib/memcpy32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmp_s.o safeclib/strcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strpbrk_s.o safeclib/strpbrk_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy_s.o safeclib/memcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldin_s.o safeclib/strcpyfldin_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strprefix_s.o safeclib/strprefix_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +In file included from src/kstring.cpp:28: +src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': +src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); + | ^~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove16_s.o safeclib/memmove16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/kopen.cpp: In function 'int ftp_open(const char*)': src/kopen.cpp:257:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 257 | memcpy_bwamem(pasv_ip, 4 * sizeof(int), v, 4 * sizeof(int), __FILE__, __LINE__); | ^~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldout_s.o safeclib/strcpyfldout_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strremovews_s.o safeclib/strremovews_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove32_s.o safeclib/memmove32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfld_s.o safeclib/strcpyfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strspn_s.o safeclib/strspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove_s.o safeclib/memmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpy_s.o safeclib/strcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strstr_s.o safeclib/strstr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/mem_primitives_lib.o safeclib/mem_primitives_lib.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcspn_s.o safeclib/strcspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtok_s.o safeclib/strtok_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstchar_s.o safeclib/strfirstchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtolowercase_s.o safeclib/strtolowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset16_s.o safeclib/memset16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstdiff_s.o safeclib/strfirstdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -3174,22 +3210,22 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -In file included from src/bwa.cpp:39: +ar rcs libsafestring.a obj/abort_handler_s.o obj/stpcpy_s.o obj/strlastsame_s.o obj/ignore_handler_s.o obj/stpncpy_s.o obj/strljustify_s.o obj/memcmp16_s.o obj/strcasecmp_s.o obj/strncat_s.o obj/memcmp32_s.o obj/strcasestr_s.o obj/strncpy_s.o obj/memcmp_s.o obj/strcat_s.o obj/strnlen_s.o obj/memcpy16_s.o obj/strcmpfld_s.o obj/strnterminate_s.o obj/memcpy32_s.o obj/strcmp_s.o obj/strpbrk_s.o obj/memcpy_s.o obj/strcpyfldin_s.o obj/strprefix_s.o obj/memmove16_s.o obj/strcpyfldout_s.o obj/strremovews_s.o obj/memmove32_s.o obj/strcpyfld_s.o obj/strspn_s.o obj/memmove_s.o obj/strcpy_s.o obj/strstr_s.o obj/mem_primitives_lib.o obj/strcspn_s.o obj/strtok_s.o obj/strfirstchar_s.o obj/strtolowercase_s.o obj/memset16_s.o obj/strfirstdiff_s.o obj/strtouppercase_s.o obj/memset32_s.o obj/strfirstsame_s.o obj/strzero_s.o obj/memset_s.o obj/strisalphanumeric_s.o obj/wcpcpy_s.o obj/memzero16_s.o obj/strisascii_s.o obj/wcscat_s.o obj/memzero32_s.o obj/strisdigit_s.o obj/wcscpy_s.o obj/memzero_s.o obj/strishex_s.o obj/wcsncat_s.o obj/strislowercase_s.o obj/wcsncpy_s.o obj/safe_mem_constraint.o obj/strismixedcase_s.o obj/wcsnlen_s.o obj/strispassword_s.o obj/wmemcmp_s.o obj/safe_str_constraint.o obj/strisuppercase_s.o obj/wmemcpy_s.o obj/strlastchar_s.o obj/wmemmove_s.o obj/snprintf_support.o obj/strlastdiff_s.o obj/wmemset_s.o +In file included from src/bwamem.h:47, + from src/kthread.h:37, + from src/kthread.cpp:32: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ -ar rcs libsafestring.a obj/abort_handler_s.o obj/stpcpy_s.o obj/strlastsame_s.o obj/ignore_handler_s.o obj/stpncpy_s.o obj/strljustify_s.o obj/memcmp16_s.o obj/strcasecmp_s.o obj/strncat_s.o obj/memcmp32_s.o obj/strcasestr_s.o obj/strncpy_s.o obj/memcmp_s.o obj/strcat_s.o obj/strnlen_s.o obj/memcpy16_s.o obj/strcmpfld_s.o obj/strnterminate_s.o obj/memcpy32_s.o obj/strcmp_s.o obj/strpbrk_s.o obj/memcpy_s.o obj/strcpyfldin_s.o obj/strprefix_s.o obj/memmove16_s.o obj/strcpyfldout_s.o obj/strremovews_s.o obj/memmove32_s.o obj/strcpyfld_s.o obj/strspn_s.o obj/memmove_s.o obj/strcpy_s.o obj/strstr_s.o obj/mem_primitives_lib.o obj/strcspn_s.o obj/strtok_s.o obj/strfirstchar_s.o obj/strtolowercase_s.o obj/memset16_s.o obj/strfirstdiff_s.o obj/strtouppercase_s.o obj/memset32_s.o obj/strfirstsame_s.o obj/strzero_s.o obj/memset_s.o obj/strisalphanumeric_s.o obj/wcpcpy_s.o obj/memzero16_s.o obj/strisascii_s.o obj/wcscat_s.o obj/memzero32_s.o obj/strisdigit_s.o obj/wcscpy_s.o obj/memzero_s.o obj/strishex_s.o obj/wcsncat_s.o obj/strislowercase_s.o obj/wcsncpy_s.o obj/safe_mem_constraint.o obj/strismixedcase_s.o obj/wcsnlen_s.o obj/strispassword_s.o obj/wmemcmp_s.o obj/safe_str_constraint.o obj/strisuppercase_s.o obj/wmemcpy_s.o obj/strlastchar_s.o obj/wmemmove_s.o obj/snprintf_support.o obj/strlastdiff_s.o obj/wmemset_s.o make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' -In file included from src/bwamem.h:47, - from src/bwamem_extra.cpp:33: +In file included from src/bwa.cpp:39: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ In file included from src/bwamem.h:47, - from src/kthread.h:37, - from src/kthread.cpp:32: + from src/bwamem_extra.cpp:33: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); @@ -3216,7 +3252,8 @@ 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ In file included from src/bwamem.h:47, - from src/bwamem.cpp:34: + from src/fastmap.h:45, + from src/fastmap.cpp:42: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); @@ -3228,6 +3265,12 @@ | | | | int int64_t {aka long int} | %ld +In file included from src/bwamem.h:47, + from src/bwamem.cpp:34: +src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': +src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); + | ^~~~~~~~ In file included from src/bwamem.h:50: src/bwamem.cpp: In function 'bwtintv_t ks_ksmall_mem_intv(size_t, bwtintv_t*, size_t)': src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] @@ -3357,13 +3400,6 @@ src/bwamem.cpp:49:1: note: in expansion of macro 'KSORT_INIT' 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ -In file included from src/bwamem.h:47, - from src/fastmap.h:45, - from src/fastmap.cpp:42: -src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': -src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); - | ^~~~~~~~ src/bwamem.cpp: In function 'mem_chain_t ks_ksmall_mem_flt(size_t, mem_chain_t*, size_t)': src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } @@ -3812,12 +3848,13 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy32_s.o safeclib/memcpy32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmp_s.o safeclib/strcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strpbrk_s.o safeclib/strpbrk_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy_s.o safeclib/memcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldin_s.o safeclib/strcpyfldin_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS In file included from src/kstring.cpp:28: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy_s.o safeclib/memcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS In file included from src/utils.cpp:44: src/utils.cpp: In function 'pair64_t ks_ksmall_128(size_t, pair64_t*, size_t)': src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] @@ -3883,6 +3920,7 @@ src/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strprefix_s.o safeclib/strprefix_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/utils.cpp: In function 'uint64_t ks_ksmall_64(size_t, uint64_t*, size_t)': src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } @@ -3947,17 +3985,8 @@ src/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldin_s.o safeclib/strcpyfldin_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strprefix_s.o safeclib/strprefix_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove16_s.o safeclib/memmove16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldout_s.o safeclib/strcpyfldout_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strremovews_s.o safeclib/strremovews_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove32_s.o safeclib/memmove32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfld_s.o safeclib/strcpyfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strspn_s.o safeclib/strspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove_s.o safeclib/memmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpy_s.o safeclib/strcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strstr_s.o safeclib/strstr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/utils.cpp: In function 'int ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)': src/kseq.h:135:109: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 135 | memcpy_bwamem(str->s + str->l, str->m - str->l, ks->buf + ks->begin, i - ks->begin, __FILE__, __LINE__); \ @@ -3971,6 +4000,13 @@ src/utils.cpp:50:1: note: in expansion of macro 'KSEQ_INIT2' 50 | KSEQ_INIT2(, gzFile, err_gzread) | ^~~~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strremovews_s.o safeclib/strremovews_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove32_s.o safeclib/memmove32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfld_s.o safeclib/strcpyfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strspn_s.o safeclib/strspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove_s.o safeclib/memmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpy_s.o safeclib/strcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strstr_s.o safeclib/strstr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/mem_primitives_lib.o safeclib/mem_primitives_lib.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcspn_s.o safeclib/strcspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtok_s.o safeclib/strtok_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -3979,15 +4015,15 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset16_s.o safeclib/memset16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstdiff_s.o safeclib/strfirstdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtouppercase_s.o safeclib/strtouppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -src/kopen.cpp: In function 'int ftp_open(const char*)': -src/kopen.cpp:257:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 257 | memcpy_bwamem(pasv_ip, 4 * sizeof(int), v, 4 * sizeof(int), __FILE__, __LINE__); - | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset32_s.o safeclib/memset32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstsame_s.o safeclib/strfirstsame_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strzero_s.o safeclib/strzero_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset_s.o safeclib/memset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisalphanumeric_s.o safeclib/strisalphanumeric_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +src/kopen.cpp: In function 'int ftp_open(const char*)': +src/kopen.cpp:257:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 257 | memcpy_bwamem(pasv_ip, 4 * sizeof(int), v, 4 * sizeof(int), __FILE__, __LINE__); + | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcpcpy_s.o safeclib/wcpcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero16_s.o safeclib/memzero16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisascii_s.o safeclib/strisascii_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -4036,8 +4072,7 @@ | ^~~~~~~~ ar rcs libsafestring.a obj/abort_handler_s.o obj/stpcpy_s.o obj/strlastsame_s.o obj/ignore_handler_s.o obj/stpncpy_s.o obj/strljustify_s.o obj/memcmp16_s.o obj/strcasecmp_s.o obj/strncat_s.o obj/memcmp32_s.o obj/strcasestr_s.o obj/strncpy_s.o obj/memcmp_s.o obj/strcat_s.o obj/strnlen_s.o obj/memcpy16_s.o obj/strcmpfld_s.o obj/strnterminate_s.o obj/memcpy32_s.o obj/strcmp_s.o obj/strpbrk_s.o obj/memcpy_s.o obj/strcpyfldin_s.o obj/strprefix_s.o obj/memmove16_s.o obj/strcpyfldout_s.o obj/strremovews_s.o obj/memmove32_s.o obj/strcpyfld_s.o obj/strspn_s.o obj/memmove_s.o obj/strcpy_s.o obj/strstr_s.o obj/mem_primitives_lib.o obj/strcspn_s.o obj/strtok_s.o obj/strfirstchar_s.o obj/strtolowercase_s.o obj/memset16_s.o obj/strfirstdiff_s.o obj/strtouppercase_s.o obj/memset32_s.o obj/strfirstsame_s.o obj/strzero_s.o obj/memset_s.o obj/strisalphanumeric_s.o obj/wcpcpy_s.o obj/memzero16_s.o obj/strisascii_s.o obj/wcscat_s.o obj/memzero32_s.o obj/strisdigit_s.o obj/wcscpy_s.o obj/memzero_s.o obj/strishex_s.o obj/wcsncat_s.o obj/strislowercase_s.o obj/wcsncpy_s.o obj/safe_mem_constraint.o obj/strismixedcase_s.o obj/wcsnlen_s.o obj/strispassword_s.o obj/wmemcmp_s.o obj/safe_str_constraint.o obj/strisuppercase_s.o obj/wmemcpy_s.o obj/strlastchar_s.o obj/wmemmove_s.o obj/snprintf_support.o obj/strlastdiff_s.o obj/wmemset_s.o make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' -In file included from src/bwamem.h:47, - from src/bwamem_extra.cpp:33: +In file included from src/bwamem_pair.cpp:36: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); @@ -4049,11 +4084,6 @@ src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ -In file included from src/bwamem_pair.cpp:36: -src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': -src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); - | ^~~~~~~~ src/bwamem_pair.cpp: In function 'int mem_matesw_batch_pre(const mem_opt_t*, const bntseq_t*, const uint8_t*, const mem_pestat_t*, const mem_alnreg_t*, int, const uint8_t*, mem_alnreg_v*, mem_cache*, int, int32_t, int32_t&, int32_t&, int32_t)': src/bwamem_pair.cpp:1028:33: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 1028 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufRefs in %s\n", @@ -4064,14 +4094,8 @@ src/bwamem_pair.cpp:1062:33: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 1062 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairs in %s\n", tid, __func__); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from src/main.h:36, - from src/main.cpp:35: -src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': -src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); - | ^~~~~~~~ In file included from src/bwamem.h:47, - from src/bwamem.cpp:34: + from src/bwamem_extra.cpp:33: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); @@ -4083,9 +4107,14 @@ | | | | int int64_t {aka long int} | %ld +In file included from src/main.h:36, + from src/main.cpp:35: +src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': +src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); + | ^~~~~~~~ In file included from src/bwamem.h:47, - from src/fastmap.h:45, - from src/fastmap.cpp:42: + from src/bwamem.cpp:34: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); @@ -4608,13 +4637,20 @@ src/bwamem.cpp:2374:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2374 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from src/bwamem.h:47, + from src/fastmap.h:45, + from src/fastmap.cpp:42: +src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': +src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); + | ^~~~~~~~ ar rcs libbwa.a src/fastmap.o src/bwtindex.o src/utils.o src/memcpy_bwamem.o src/kthread.o src/kstring.o src/ksw.o src/bntseq.o src/bwamem.o src/profiling.o src/bandedSWA.o src/FMI_search.o src/read_index_ele.o src/bwamem_pair.o src/kswv.o src/bwa.o src/bwamem_extra.o src/kopen.o g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now src/main.o libbwa.a -lpthread -lm -lz -L. -lbwa -Lext/safestringlib -lsafestring -o bwa-mem2.avx512bw make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -Wall -O3 src/runsimd.cpp -Iext/safestringlib/include -Lext/safestringlib/ -lsafestring -o bwa-mem2 make[2]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1' dh_auto_build -- multi - make -j40 "INSTALL=install --strip-program=true" multi + make -j42 "INSTALL=install --strip-program=true" multi make[2]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1' rm -f src/*.o libbwa.a; cd ext/safestringlib/ && make clean; make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' @@ -4672,12 +4708,13 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy32_s.o safeclib/memcpy32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmp_s.o safeclib/strcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strpbrk_s.o safeclib/strpbrk_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy_s.o safeclib/memcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldin_s.o safeclib/strcpyfldin_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS In file included from src/kstring.cpp:28: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy_s.o safeclib/memcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS In file included from src/utils.cpp:44: src/utils.cpp: In function 'pair64_t ks_ksmall_128(size_t, pair64_t*, size_t)': src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] @@ -4743,6 +4780,8 @@ src/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strprefix_s.o safeclib/strprefix_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove16_s.o safeclib/memmove16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/utils.cpp: In function 'uint64_t ks_ksmall_64(size_t, uint64_t*, size_t)': src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } @@ -4807,15 +4846,11 @@ src/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldin_s.o safeclib/strcpyfldin_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strprefix_s.o safeclib/strprefix_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove16_s.o safeclib/memmove16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldout_s.o safeclib/strcpyfldout_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strremovews_s.o safeclib/strremovews_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove32_s.o safeclib/memmove32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfld_s.o safeclib/strcpyfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strspn_s.o safeclib/strspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove_s.o safeclib/memmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/utils.cpp: In function 'int ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)': src/kseq.h:135:109: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 135 | memcpy_bwamem(str->s + str->l, str->m - str->l, ks->buf + ks->begin, i - ks->begin, __FILE__, __LINE__); \ @@ -4829,6 +4864,7 @@ src/utils.cpp:50:1: note: in expansion of macro 'KSEQ_INIT2' 50 | KSEQ_INIT2(, gzFile, err_gzread) | ^~~~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove_s.o safeclib/memmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpy_s.o safeclib/strcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strstr_s.o safeclib/strstr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/mem_primitives_lib.o safeclib/mem_primitives_lib.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -4839,15 +4875,16 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset16_s.o safeclib/memset16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstdiff_s.o safeclib/strfirstdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtouppercase_s.o safeclib/strtouppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -src/kopen.cpp: In function 'int ftp_open(const char*)': -src/kopen.cpp:257:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 257 | memcpy_bwamem(pasv_ip, 4 * sizeof(int), v, 4 * sizeof(int), __FILE__, __LINE__); - | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset32_s.o safeclib/memset32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstsame_s.o safeclib/strfirstsame_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strzero_s.o safeclib/strzero_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset_s.o safeclib/memset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisalphanumeric_s.o safeclib/strisalphanumeric_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +In file included from src/bwa.cpp:39: +src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': +src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); + | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcpcpy_s.o safeclib/wcpcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero16_s.o safeclib/memzero16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisascii_s.o safeclib/strisascii_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -4858,6 +4895,10 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero_s.o safeclib/memzero_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strishex_s.o safeclib/strishex_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsncat_s.o safeclib/wcsncat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +src/kopen.cpp: In function 'int ftp_open(const char*)': +src/kopen.cpp:257:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 257 | memcpy_bwamem(pasv_ip, 4 * sizeof(int), v, 4 * sizeof(int), __FILE__, __LINE__); + | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strislowercase_s.o safeclib/strislowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsncpy_s.o safeclib/wcsncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/safe_mem_constraint.o safeclib/safe_mem_constraint.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -4889,27 +4930,28 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -In file included from src/bwa.cpp:39: +ar rcs libsafestring.a obj/abort_handler_s.o obj/stpcpy_s.o obj/strlastsame_s.o obj/ignore_handler_s.o obj/stpncpy_s.o obj/strljustify_s.o obj/memcmp16_s.o obj/strcasecmp_s.o obj/strncat_s.o obj/memcmp32_s.o obj/strcasestr_s.o obj/strncpy_s.o obj/memcmp_s.o obj/strcat_s.o obj/strnlen_s.o obj/memcpy16_s.o obj/strcmpfld_s.o obj/strnterminate_s.o obj/memcpy32_s.o obj/strcmp_s.o obj/strpbrk_s.o obj/memcpy_s.o obj/strcpyfldin_s.o obj/strprefix_s.o obj/memmove16_s.o obj/strcpyfldout_s.o obj/strremovews_s.o obj/memmove32_s.o obj/strcpyfld_s.o obj/strspn_s.o obj/memmove_s.o obj/strcpy_s.o obj/strstr_s.o obj/mem_primitives_lib.o obj/strcspn_s.o obj/strtok_s.o obj/strfirstchar_s.o obj/strtolowercase_s.o obj/memset16_s.o obj/strfirstdiff_s.o obj/strtouppercase_s.o obj/memset32_s.o obj/strfirstsame_s.o obj/strzero_s.o obj/memset_s.o obj/strisalphanumeric_s.o obj/wcpcpy_s.o obj/memzero16_s.o obj/strisascii_s.o obj/wcscat_s.o obj/memzero32_s.o obj/strisdigit_s.o obj/wcscpy_s.o obj/memzero_s.o obj/strishex_s.o obj/wcsncat_s.o obj/strislowercase_s.o obj/wcsncpy_s.o obj/safe_mem_constraint.o obj/strismixedcase_s.o obj/wcsnlen_s.o obj/strispassword_s.o obj/wmemcmp_s.o obj/safe_str_constraint.o obj/strisuppercase_s.o obj/wmemcpy_s.o obj/strlastchar_s.o obj/wmemmove_s.o obj/snprintf_support.o obj/strlastdiff_s.o obj/wmemset_s.o +make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' +In file included from src/main.h:36, + from src/main.cpp:35: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ -ar rcs libsafestring.a obj/abort_handler_s.o obj/stpcpy_s.o obj/strlastsame_s.o obj/ignore_handler_s.o obj/stpncpy_s.o obj/strljustify_s.o obj/memcmp16_s.o obj/strcasecmp_s.o obj/strncat_s.o obj/memcmp32_s.o obj/strcasestr_s.o obj/strncpy_s.o obj/memcmp_s.o obj/strcat_s.o obj/strnlen_s.o obj/memcpy16_s.o obj/strcmpfld_s.o obj/strnterminate_s.o obj/memcpy32_s.o obj/strcmp_s.o obj/strpbrk_s.o obj/memcpy_s.o obj/strcpyfldin_s.o obj/strprefix_s.o obj/memmove16_s.o obj/strcpyfldout_s.o obj/strremovews_s.o obj/memmove32_s.o obj/strcpyfld_s.o obj/strspn_s.o obj/memmove_s.o obj/strcpy_s.o obj/strstr_s.o obj/mem_primitives_lib.o obj/strcspn_s.o obj/strtok_s.o obj/strfirstchar_s.o obj/strtolowercase_s.o obj/memset16_s.o obj/strfirstdiff_s.o obj/strtouppercase_s.o obj/memset32_s.o obj/strfirstsame_s.o obj/strzero_s.o obj/memset_s.o obj/strisalphanumeric_s.o obj/wcpcpy_s.o obj/memzero16_s.o obj/strisascii_s.o obj/wcscat_s.o obj/memzero32_s.o obj/strisdigit_s.o obj/wcscpy_s.o obj/memzero_s.o obj/strishex_s.o obj/wcsncat_s.o obj/strislowercase_s.o obj/wcsncpy_s.o obj/safe_mem_constraint.o obj/strismixedcase_s.o obj/wcsnlen_s.o obj/strispassword_s.o obj/wmemcmp_s.o obj/safe_str_constraint.o obj/strisuppercase_s.o obj/wmemcpy_s.o obj/strlastchar_s.o obj/wmemmove_s.o obj/snprintf_support.o obj/strlastdiff_s.o obj/wmemset_s.o -make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' In file included from src/bwamem.h:47, from src/bwamem_extra.cpp:33: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ -In file included from src/bwamem_pair.cpp:36: +In file included from src/bwamem.h:47, + from src/kthread.h:37, + from src/kthread.cpp:32: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ -In file included from src/bwamem.h:47, - from src/kthread.h:37, - from src/kthread.cpp:32: +In file included from src/bwamem_pair.cpp:36: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); @@ -4924,8 +4966,9 @@ src/bwamem_pair.cpp:1062:33: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 1062 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairs in %s\n", tid, __func__); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from src/main.h:36, - from src/main.cpp:35: +In file included from src/bwamem.h:47, + from src/fastmap.h:45, + from src/fastmap.cpp:42: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); @@ -4981,13 +5024,6 @@ src/bwamem.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ -In file included from src/bwamem.h:47, - from src/fastmap.h:45, - from src/fastmap.cpp:42: -src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': -src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); - | ^~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ @@ -5527,25 +5563,11 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy32_s.o safeclib/memcpy32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmp_s.o safeclib/strcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strpbrk_s.o safeclib/strpbrk_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -In file included from src/kstring.cpp:28: -src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': -src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); - | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy_s.o safeclib/memcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldin_s.o safeclib/strcpyfldin_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strprefix_s.o safeclib/strprefix_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove16_s.o safeclib/memmove16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldout_s.o safeclib/strcpyfldout_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strremovews_s.o safeclib/strremovews_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove32_s.o safeclib/memmove32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfld_s.o safeclib/strcpyfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strspn_s.o safeclib/strspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove_s.o safeclib/memmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpy_s.o safeclib/strcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strstr_s.o safeclib/strstr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/mem_primitives_lib.o safeclib/mem_primitives_lib.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcspn_s.o safeclib/strcspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS In file included from src/utils.cpp:44: src/utils.cpp: In function 'pair64_t ks_ksmall_128(size_t, pair64_t*, size_t)': src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] @@ -5611,10 +5633,6 @@ src/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ -src/kopen.cpp: In function 'int ftp_open(const char*)': -src/kopen.cpp:257:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 257 | memcpy_bwamem(pasv_ip, 4 * sizeof(int), v, 4 * sizeof(int), __FILE__, __LINE__); - | ^~~~~~~~ src/utils.cpp: In function 'uint64_t ks_ksmall_64(size_t, uint64_t*, size_t)': src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } @@ -5625,6 +5643,7 @@ src/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strremovews_s.o safeclib/strremovews_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ @@ -5679,6 +5698,17 @@ src/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ +In file included from src/kstring.cpp:28: +src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': +src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); + | ^~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove32_s.o safeclib/memmove32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfld_s.o safeclib/strcpyfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strspn_s.o safeclib/strspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove_s.o safeclib/memmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpy_s.o safeclib/strcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strstr_s.o safeclib/strstr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/utils.cpp: In function 'int ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)': src/kseq.h:135:109: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 135 | memcpy_bwamem(str->s + str->l, str->m - str->l, ks->buf + ks->begin, i - ks->begin, __FILE__, __LINE__); \ @@ -5692,6 +5722,8 @@ src/utils.cpp:50:1: note: in expansion of macro 'KSEQ_INIT2' 50 | KSEQ_INIT2(, gzFile, err_gzread) | ^~~~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/mem_primitives_lib.o safeclib/mem_primitives_lib.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcspn_s.o safeclib/strcspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtok_s.o safeclib/strtok_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstchar_s.o safeclib/strfirstchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtolowercase_s.o safeclib/strtolowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -5709,6 +5741,10 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcscat_s.o safeclib/wcscat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero32_s.o safeclib/memzero32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisdigit_s.o safeclib/strisdigit_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +src/kopen.cpp: In function 'int ftp_open(const char*)': +src/kopen.cpp:257:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 257 | memcpy_bwamem(pasv_ip, 4 * sizeof(int), v, 4 * sizeof(int), __FILE__, __LINE__); + | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcscpy_s.o safeclib/wcscpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero_s.o safeclib/memzero_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strishex_s.o safeclib/strishex_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -5726,6 +5762,8 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastchar_s.o safeclib/strlastchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemmove_s.o safeclib/wmemmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/snprintf_support.o safeclib/snprintf_support.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastdiff_s.o safeclib/strlastdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemset_s.o safeclib/wmemset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/kopen.cpp: In function 'void* kopen(const char*, int*)': src/kopen.cpp:262:27: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 262 | sprintf(port2, "%d", pasv_port); @@ -5742,22 +5780,22 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastdiff_s.o safeclib/strlastdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -In file included from src/bwa.cpp:39: +In file included from src/bwamem.h:47, + from src/kthread.h:37, + from src/kthread.cpp:32: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemset_s.o safeclib/wmemset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -In file included from src/bwamem.h:47, - from src/bwamem_extra.cpp:33: +In file included from src/bwa.cpp:39: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ +ar rcs libsafestring.a obj/abort_handler_s.o obj/stpcpy_s.o obj/strlastsame_s.o obj/ignore_handler_s.o obj/stpncpy_s.o obj/strljustify_s.o obj/memcmp16_s.o obj/strcasecmp_s.o obj/strncat_s.o obj/memcmp32_s.o obj/strcasestr_s.o obj/strncpy_s.o obj/memcmp_s.o obj/strcat_s.o obj/strnlen_s.o obj/memcpy16_s.o obj/strcmpfld_s.o obj/strnterminate_s.o obj/memcpy32_s.o obj/strcmp_s.o obj/strpbrk_s.o obj/memcpy_s.o obj/strcpyfldin_s.o obj/strprefix_s.o obj/memmove16_s.o obj/strcpyfldout_s.o obj/strremovews_s.o obj/memmove32_s.o obj/strcpyfld_s.o obj/strspn_s.o obj/memmove_s.o obj/strcpy_s.o obj/strstr_s.o obj/mem_primitives_lib.o obj/strcspn_s.o obj/strtok_s.o obj/strfirstchar_s.o obj/strtolowercase_s.o obj/memset16_s.o obj/strfirstdiff_s.o obj/strtouppercase_s.o obj/memset32_s.o obj/strfirstsame_s.o obj/strzero_s.o obj/memset_s.o obj/strisalphanumeric_s.o obj/wcpcpy_s.o obj/memzero16_s.o obj/strisascii_s.o obj/wcscat_s.o obj/memzero32_s.o obj/strisdigit_s.o obj/wcscpy_s.o obj/memzero_s.o obj/strishex_s.o obj/wcsncat_s.o obj/strislowercase_s.o obj/wcsncpy_s.o obj/safe_mem_constraint.o obj/strismixedcase_s.o obj/wcsnlen_s.o obj/strispassword_s.o obj/wmemcmp_s.o obj/safe_str_constraint.o obj/strisuppercase_s.o obj/wmemcpy_s.o obj/strlastchar_s.o obj/wmemmove_s.o obj/snprintf_support.o obj/strlastdiff_s.o obj/wmemset_s.o +make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' In file included from src/bwamem.h:47, - from src/kthread.h:37, - from src/kthread.cpp:32: + from src/bwamem_extra.cpp:33: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); @@ -5767,8 +5805,6 @@ src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ -ar rcs libsafestring.a obj/abort_handler_s.o obj/stpcpy_s.o obj/strlastsame_s.o obj/ignore_handler_s.o obj/stpncpy_s.o obj/strljustify_s.o obj/memcmp16_s.o obj/strcasecmp_s.o obj/strncat_s.o obj/memcmp32_s.o obj/strcasestr_s.o obj/strncpy_s.o obj/memcmp_s.o obj/strcat_s.o obj/strnlen_s.o obj/memcpy16_s.o obj/strcmpfld_s.o obj/strnterminate_s.o obj/memcpy32_s.o obj/strcmp_s.o obj/strpbrk_s.o obj/memcpy_s.o obj/strcpyfldin_s.o obj/strprefix_s.o obj/memmove16_s.o obj/strcpyfldout_s.o obj/strremovews_s.o obj/memmove32_s.o obj/strcpyfld_s.o obj/strspn_s.o obj/memmove_s.o obj/strcpy_s.o obj/strstr_s.o obj/mem_primitives_lib.o obj/strcspn_s.o obj/strtok_s.o obj/strfirstchar_s.o obj/strtolowercase_s.o obj/memset16_s.o obj/strfirstdiff_s.o obj/strtouppercase_s.o obj/memset32_s.o obj/strfirstsame_s.o obj/strzero_s.o obj/memset_s.o obj/strisalphanumeric_s.o obj/wcpcpy_s.o obj/memzero16_s.o obj/strisascii_s.o obj/wcscat_s.o obj/memzero32_s.o obj/strisdigit_s.o obj/wcscpy_s.o obj/memzero_s.o obj/strishex_s.o obj/wcsncat_s.o obj/strislowercase_s.o obj/wcsncpy_s.o obj/safe_mem_constraint.o obj/strismixedcase_s.o obj/wcsnlen_s.o obj/strispassword_s.o obj/wmemcmp_s.o obj/safe_str_constraint.o obj/strisuppercase_s.o obj/wmemcpy_s.o obj/strlastchar_s.o obj/wmemmove_s.o obj/snprintf_support.o obj/strlastdiff_s.o obj/wmemset_s.o -make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' src/bwamem_pair.cpp: In function 'int mem_matesw_batch_pre(const mem_opt_t*, const bntseq_t*, const uint8_t*, const mem_pestat_t*, const mem_alnreg_t*, int, const uint8_t*, mem_alnreg_v*, mem_cache*, int, int32_t, int32_t&, int32_t&, int32_t)': src/bwamem_pair.cpp:1028:33: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 1028 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufRefs in %s\n", @@ -6382,17 +6418,15 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy32_s.o safeclib/memcpy32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmp_s.o safeclib/strcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strpbrk_s.o safeclib/strpbrk_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy_s.o safeclib/memcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldin_s.o safeclib/strcpyfldin_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS In file included from src/kstring.cpp:28: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy_s.o safeclib/memcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldin_s.o safeclib/strcpyfldin_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strprefix_s.o safeclib/strprefix_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove16_s.o safeclib/memmove16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldout_s.o safeclib/strcpyfldout_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strremovews_s.o safeclib/strremovews_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS In file included from src/utils.cpp:44: src/utils.cpp: In function 'pair64_t ks_ksmall_128(size_t, pair64_t*, size_t)': src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] @@ -6449,6 +6483,10 @@ src/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ +src/kopen.cpp: In function 'int ftp_open(const char*)': +src/kopen.cpp:257:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 257 | memcpy_bwamem(pasv_ip, 4 * sizeof(int), v, 4 * sizeof(int), __FILE__, __LINE__); + | ^~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ @@ -6458,9 +6496,6 @@ src/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove32_s.o safeclib/memmove32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfld_s.o safeclib/strcpyfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strspn_s.o safeclib/strspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/utils.cpp: In function 'uint64_t ks_ksmall_64(size_t, uint64_t*, size_t)': src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } @@ -6471,6 +6506,7 @@ src/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldout_s.o safeclib/strcpyfldout_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ @@ -6525,17 +6561,9 @@ src/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove_s.o safeclib/memmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpy_s.o safeclib/strcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strstr_s.o safeclib/strstr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/mem_primitives_lib.o safeclib/mem_primitives_lib.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcspn_s.o safeclib/strcspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtok_s.o safeclib/strtok_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstchar_s.o safeclib/strfirstchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtolowercase_s.o safeclib/strtolowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset16_s.o safeclib/memset16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstdiff_s.o safeclib/strfirstdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtouppercase_s.o safeclib/strtouppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strremovews_s.o safeclib/strremovews_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove32_s.o safeclib/memmove32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfld_s.o safeclib/strcpyfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/utils.cpp: In function 'int ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)': src/kseq.h:135:109: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 135 | memcpy_bwamem(str->s + str->l, str->m - str->l, ks->buf + ks->begin, i - ks->begin, __FILE__, __LINE__); \ @@ -6549,10 +6577,34 @@ src/utils.cpp:50:1: note: in expansion of macro 'KSEQ_INIT2' 50 | KSEQ_INIT2(, gzFile, err_gzread) | ^~~~~~~~~~ -src/kopen.cpp: In function 'int ftp_open(const char*)': -src/kopen.cpp:257:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 257 | memcpy_bwamem(pasv_ip, 4 * sizeof(int), v, 4 * sizeof(int), __FILE__, __LINE__); - | ^~~~~~~~ +src/kopen.cpp: In function 'void* kopen(const char*, int*)': +src/kopen.cpp:262:27: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] + 262 | sprintf(port2, "%d", pasv_port); + | ^ +In file included from /usr/include/stdio.h:970, + from src/kopen.cpp:30: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'int ftp_open(const char*)' at src/kopen.cpp:262:9, + inlined from 'void* kopen(const char*, int*)' at src/kopen.cpp:325:21: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 10 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strspn_s.o safeclib/strspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove_s.o safeclib/memmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpy_s.o safeclib/strcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strstr_s.o safeclib/strstr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/mem_primitives_lib.o safeclib/mem_primitives_lib.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcspn_s.o safeclib/strcspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtok_s.o safeclib/strtok_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstchar_s.o safeclib/strfirstchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtolowercase_s.o safeclib/strtolowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset16_s.o safeclib/memset16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstdiff_s.o safeclib/strfirstdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtouppercase_s.o safeclib/strtouppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset32_s.o safeclib/memset32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstsame_s.o safeclib/strfirstsame_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strzero_s.o safeclib/strzero_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -6583,22 +6635,6 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/snprintf_support.o safeclib/snprintf_support.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastdiff_s.o safeclib/strlastdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemset_s.o safeclib/wmemset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -src/kopen.cpp: In function 'void* kopen(const char*, int*)': -src/kopen.cpp:262:27: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] - 262 | sprintf(port2, "%d", pasv_port); - | ^ -In file included from /usr/include/stdio.h:970, - from src/kopen.cpp:30: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'int ftp_open(const char*)' at src/kopen.cpp:262:9, - inlined from 'void* kopen(const char*, int*)' at src/kopen.cpp:325:21: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 10 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ ar rcs libsafestring.a obj/abort_handler_s.o obj/stpcpy_s.o obj/strlastsame_s.o obj/ignore_handler_s.o obj/stpncpy_s.o obj/strljustify_s.o obj/memcmp16_s.o obj/strcasecmp_s.o obj/strncat_s.o obj/memcmp32_s.o obj/strcasestr_s.o obj/strncpy_s.o obj/memcmp_s.o obj/strcat_s.o obj/strnlen_s.o obj/memcpy16_s.o obj/strcmpfld_s.o obj/strnterminate_s.o obj/memcpy32_s.o obj/strcmp_s.o obj/strpbrk_s.o obj/memcpy_s.o obj/strcpyfldin_s.o obj/strprefix_s.o obj/memmove16_s.o obj/strcpyfldout_s.o obj/strremovews_s.o obj/memmove32_s.o obj/strcpyfld_s.o obj/strspn_s.o obj/memmove_s.o obj/strcpy_s.o obj/strstr_s.o obj/mem_primitives_lib.o obj/strcspn_s.o obj/strtok_s.o obj/strfirstchar_s.o obj/strtolowercase_s.o obj/memset16_s.o obj/strfirstdiff_s.o obj/strtouppercase_s.o obj/memset32_s.o obj/strfirstsame_s.o obj/strzero_s.o obj/memset_s.o obj/strisalphanumeric_s.o obj/wcpcpy_s.o obj/memzero16_s.o obj/strisascii_s.o obj/wcscat_s.o obj/memzero32_s.o obj/strisdigit_s.o obj/wcscpy_s.o obj/memzero_s.o obj/strishex_s.o obj/wcsncat_s.o obj/strislowercase_s.o obj/wcsncpy_s.o obj/safe_mem_constraint.o obj/strismixedcase_s.o obj/wcsnlen_s.o obj/strispassword_s.o obj/wmemcmp_s.o obj/safe_str_constraint.o obj/strisuppercase_s.o obj/wmemcpy_s.o obj/strlastchar_s.o obj/wmemmove_s.o obj/snprintf_support.o obj/strlastdiff_s.o obj/wmemset_s.o make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' In file included from src/bwamem_pair.cpp:36: @@ -6606,13 +6642,8 @@ src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ -In file included from src/main.h:36, - from src/main.cpp:35: -src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': -src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); - | ^~~~~~~~ -In file included from src/bwa.cpp:39: +In file included from src/bwamem.h:47, + from src/bwamem.cpp:34: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); @@ -6624,42 +6655,11 @@ src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ -In file included from src/bwamem.h:47, - from src/bwamem_extra.cpp:33: -src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': -src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); - | ^~~~~~~~ -In file included from src/bwamem.h:47, - from src/bwamem.cpp:34: -src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': -src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); - | ^~~~~~~~ -src/FMI_search.cpp: In member function 'int FMI_search::build_fm_index(const char*, char*, int64_t, int64_t*, int64_t*)': -src/FMI_search.cpp:278:28: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=] - 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); - | ~^ ~~~ - | | | - | int int64_t {aka long int} - | %ld -In file included from src/bwamem.h:47, - from src/fastmap.h:45, - from src/fastmap.cpp:42: +In file included from src/bwa.cpp:39: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ -src/bwamem_pair.cpp: In function 'int mem_matesw_batch_pre(const mem_opt_t*, const bntseq_t*, const uint8_t*, const mem_pestat_t*, const mem_alnreg_t*, int, const uint8_t*, mem_alnreg_v*, mem_cache*, int, int32_t, int32_t&, int32_t&, int32_t)': -src/bwamem_pair.cpp:1028:33: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] - 1028 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufRefs in %s\n", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -src/bwamem_pair.cpp:1045:33: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] - 1045 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufQers in %s\n", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -src/bwamem_pair.cpp:1062:33: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] - 1062 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairs in %s\n", tid, __func__); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from src/bwamem.h:50: src/bwamem.cpp: In function 'bwtintv_t ks_ksmall_mem_intv(size_t, bwtintv_t*, size_t)': src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] @@ -7113,6 +7113,12 @@ src/bwamem.cpp:388:117: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 388 | memcpy_bwamem((char*) (auxSeedBuf), c->m * sizeof(mem_seed_t), c->seeds, c->n * sizeof(mem_seed_t), __FILE__, __LINE__); | ^~~~~~~~ +In file included from src/main.h:36, + from src/main.cpp:35: +src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': +src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); + | ^~~~~~~~ src/bwamem.cpp: In function 'SMEM* mem_collect_smem(FMI_search*, const mem_opt_t*, const bseq1_t*, int, SMEM*, int32_t*, int16_t*, uint8_t*, int32_t*, mem_cache*, int64_t&, int)': src/bwamem.cpp:654:25: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 654 | fprintf(stderr, "[%0.4d] REA Re-allocating enc_qdb only\n", tid); @@ -7178,6 +7184,36 @@ src/bwamem.cpp:2374:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2374 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from src/bwamem.h:47, + from src/bwamem_extra.cpp:33: +src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': +src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); + | ^~~~~~~~ +In file included from src/bwamem.h:47, + from src/fastmap.h:45, + from src/fastmap.cpp:42: +src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': +src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); + | ^~~~~~~~ +src/bwamem_pair.cpp: In function 'int mem_matesw_batch_pre(const mem_opt_t*, const bntseq_t*, const uint8_t*, const mem_pestat_t*, const mem_alnreg_t*, int, const uint8_t*, mem_alnreg_v*, mem_cache*, int, int32_t, int32_t&, int32_t&, int32_t)': +src/bwamem_pair.cpp:1028:33: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] + 1028 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufRefs in %s\n", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +src/bwamem_pair.cpp:1045:33: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] + 1045 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufQers in %s\n", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +src/bwamem_pair.cpp:1062:33: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] + 1062 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairs in %s\n", tid, __func__); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +src/FMI_search.cpp: In member function 'int FMI_search::build_fm_index(const char*, char*, int64_t, int64_t*, int64_t*)': +src/FMI_search.cpp:278:28: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=] + 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); + | ~^ ~~~ + | | | + | int int64_t {aka long int} + | %ld ar rcs libbwa.a src/fastmap.o src/bwtindex.o src/utils.o src/memcpy_bwamem.o src/kthread.o src/kstring.o src/ksw.o src/bntseq.o src/bwamem.o src/profiling.o src/bandedSWA.o src/FMI_search.o src/read_index_ele.o src/bwamem_pair.o src/kswv.o src/bwa.o src/bwamem_extra.o src/kopen.o g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now src/main.o libbwa.a -lpthread -lm -lz -L. -lbwa -Lext/safestringlib -lsafestring -o bwa-mem2.avx make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1' @@ -7237,13 +7273,21 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy32_s.o safeclib/memcpy32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmp_s.o safeclib/strcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strpbrk_s.o safeclib/strpbrk_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy_s.o safeclib/memcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldin_s.o safeclib/strcpyfldin_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strprefix_s.o safeclib/strprefix_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove16_s.o safeclib/memmove16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldout_s.o safeclib/strcpyfldout_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strremovews_s.o safeclib/strremovews_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS In file included from src/kstring.cpp:28: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy_s.o safeclib/memcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldin_s.o safeclib/strcpyfldin_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove32_s.o safeclib/memmove32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfld_s.o safeclib/strcpyfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strspn_s.o safeclib/strspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove_s.o safeclib/memmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS In file included from src/utils.cpp:44: src/utils.cpp: In function 'pair64_t ks_ksmall_128(size_t, pair64_t*, size_t)': src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] @@ -7309,6 +7353,7 @@ src/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpy_s.o safeclib/strcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/utils.cpp: In function 'uint64_t ks_ksmall_64(size_t, uint64_t*, size_t)': src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } @@ -7319,7 +7364,6 @@ src/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strprefix_s.o safeclib/strprefix_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ @@ -7374,18 +7418,20 @@ src/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove16_s.o safeclib/memmove16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldout_s.o safeclib/strcpyfldout_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strremovews_s.o safeclib/strremovews_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove32_s.o safeclib/memmove32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfld_s.o safeclib/strcpyfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strspn_s.o safeclib/strspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove_s.o safeclib/memmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpy_s.o safeclib/strcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strstr_s.o safeclib/strstr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +src/kopen.cpp: In function 'int ftp_open(const char*)': +src/kopen.cpp:257:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 257 | memcpy_bwamem(pasv_ip, 4 * sizeof(int), v, 4 * sizeof(int), __FILE__, __LINE__); + | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/mem_primitives_lib.o safeclib/mem_primitives_lib.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcspn_s.o safeclib/strcspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtok_s.o safeclib/strtok_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstchar_s.o safeclib/strfirstchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtolowercase_s.o safeclib/strtolowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset16_s.o safeclib/memset16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstdiff_s.o safeclib/strfirstdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtouppercase_s.o safeclib/strtouppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset32_s.o safeclib/memset32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/utils.cpp: In function 'int ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)': src/kseq.h:135:109: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 135 | memcpy_bwamem(str->s + str->l, str->m - str->l, ks->buf + ks->begin, i - ks->begin, __FILE__, __LINE__); \ @@ -7399,17 +7445,7 @@ src/utils.cpp:50:1: note: in expansion of macro 'KSEQ_INIT2' 50 | KSEQ_INIT2(, gzFile, err_gzread) | ^~~~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstchar_s.o safeclib/strfirstchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtolowercase_s.o safeclib/strtolowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset16_s.o safeclib/memset16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstdiff_s.o safeclib/strfirstdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtouppercase_s.o safeclib/strtouppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset32_s.o safeclib/memset32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstsame_s.o safeclib/strfirstsame_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -src/kopen.cpp: In function 'int ftp_open(const char*)': -src/kopen.cpp:257:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 257 | memcpy_bwamem(pasv_ip, 4 * sizeof(int), v, 4 * sizeof(int), __FILE__, __LINE__); - | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strzero_s.o safeclib/strzero_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset_s.o safeclib/memset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisalphanumeric_s.o safeclib/strisalphanumeric_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -7423,21 +7459,6 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero_s.o safeclib/memzero_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strishex_s.o safeclib/strishex_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsncat_s.o safeclib/wcsncat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strislowercase_s.o safeclib/strislowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsncpy_s.o safeclib/wcsncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/safe_mem_constraint.o safeclib/safe_mem_constraint.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strismixedcase_s.o safeclib/strismixedcase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsnlen_s.o safeclib/wcsnlen_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strispassword_s.o safeclib/strispassword_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemcmp_s.o safeclib/wmemcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/safe_str_constraint.o safeclib/safe_str_constraint.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisuppercase_s.o safeclib/strisuppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemcpy_s.o safeclib/wmemcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastchar_s.o safeclib/strlastchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemmove_s.o safeclib/wmemmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/snprintf_support.o safeclib/snprintf_support.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastdiff_s.o safeclib/strlastdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemset_s.o safeclib/wmemset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/kopen.cpp: In function 'void* kopen(const char*, int*)': src/kopen.cpp:262:27: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 262 | sprintf(port2, "%d", pasv_port); @@ -7454,6 +7475,21 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strislowercase_s.o safeclib/strislowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsncpy_s.o safeclib/wcsncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/safe_mem_constraint.o safeclib/safe_mem_constraint.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strismixedcase_s.o safeclib/strismixedcase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsnlen_s.o safeclib/wcsnlen_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strispassword_s.o safeclib/strispassword_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemcmp_s.o safeclib/wmemcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/safe_str_constraint.o safeclib/safe_str_constraint.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisuppercase_s.o safeclib/strisuppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemcpy_s.o safeclib/wmemcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastchar_s.o safeclib/strlastchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemmove_s.o safeclib/wmemmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/snprintf_support.o safeclib/snprintf_support.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastdiff_s.o safeclib/strlastdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemset_s.o safeclib/wmemset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS ar rcs libsafestring.a obj/abort_handler_s.o obj/stpcpy_s.o obj/strlastsame_s.o obj/ignore_handler_s.o obj/stpncpy_s.o obj/strljustify_s.o obj/memcmp16_s.o obj/strcasecmp_s.o obj/strncat_s.o obj/memcmp32_s.o obj/strcasestr_s.o obj/strncpy_s.o obj/memcmp_s.o obj/strcat_s.o obj/strnlen_s.o obj/memcpy16_s.o obj/strcmpfld_s.o obj/strnterminate_s.o obj/memcpy32_s.o obj/strcmp_s.o obj/strpbrk_s.o obj/memcpy_s.o obj/strcpyfldin_s.o obj/strprefix_s.o obj/memmove16_s.o obj/strcpyfldout_s.o obj/strremovews_s.o obj/memmove32_s.o obj/strcpyfld_s.o obj/strspn_s.o obj/memmove_s.o obj/strcpy_s.o obj/strstr_s.o obj/mem_primitives_lib.o obj/strcspn_s.o obj/strtok_s.o obj/strfirstchar_s.o obj/strtolowercase_s.o obj/memset16_s.o obj/strfirstdiff_s.o obj/strtouppercase_s.o obj/memset32_s.o obj/strfirstsame_s.o obj/strzero_s.o obj/memset_s.o obj/strisalphanumeric_s.o obj/wcpcpy_s.o obj/memzero16_s.o obj/strisascii_s.o obj/wcscat_s.o obj/memzero32_s.o obj/strisdigit_s.o obj/wcscpy_s.o obj/memzero_s.o obj/strishex_s.o obj/wcsncat_s.o obj/strislowercase_s.o obj/wcsncpy_s.o obj/safe_mem_constraint.o obj/strismixedcase_s.o obj/wcsnlen_s.o obj/strispassword_s.o obj/wmemcmp_s.o obj/safe_str_constraint.o obj/strisuppercase_s.o obj/wmemcpy_s.o obj/strlastchar_s.o obj/wmemmove_s.o obj/snprintf_support.o obj/strlastdiff_s.o obj/wmemset_s.o make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' In file included from src/bwamem_pair.cpp:36: @@ -7461,20 +7497,8 @@ src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ -In file included from src/main.h:36, - from src/main.cpp:35: -src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': -src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); - | ^~~~~~~~ -In file included from src/bwa.cpp:39: -src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': -src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); - | ^~~~~~~~ In file included from src/bwamem.h:47, - from src/kthread.h:37, - from src/kthread.cpp:32: + from src/bwamem.cpp:34: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); @@ -7485,12 +7509,6 @@ src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ -In file included from src/bwamem.h:47, - from src/bwamem.cpp:34: -src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': -src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); - | ^~~~~~~~ src/FMI_search.cpp: In member function 'int FMI_search::build_fm_index(const char*, char*, int64_t, int64_t*, int64_t*)': src/FMI_search.cpp:278:28: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=] 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); @@ -7498,23 +7516,12 @@ | | | | int int64_t {aka long int} | %ld -In file included from src/bwamem.h:47, - from src/fastmap.h:45, - from src/fastmap.cpp:42: +In file included from src/main.h:36, + from src/main.cpp:35: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ -src/bwamem_pair.cpp: In function 'int mem_matesw_batch_pre(const mem_opt_t*, const bntseq_t*, const uint8_t*, const mem_pestat_t*, const mem_alnreg_t*, int, const uint8_t*, mem_alnreg_v*, mem_cache*, int, int32_t, int32_t&, int32_t&, int32_t)': -src/bwamem_pair.cpp:1028:33: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] - 1028 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufRefs in %s\n", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -src/bwamem_pair.cpp:1045:33: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] - 1045 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufQers in %s\n", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -src/bwamem_pair.cpp:1062:33: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] - 1062 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairs in %s\n", tid, __func__); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from src/bwamem.h:50: src/bwamem.cpp: In function 'bwtintv_t ks_ksmall_mem_intv(size_t, bwtintv_t*, size_t)': src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] @@ -8033,6 +8040,35 @@ src/bwamem.cpp:2374:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2374 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from src/bwamem.h:47, + from src/kthread.h:37, + from src/kthread.cpp:32: +src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': +src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); + | ^~~~~~~~ +In file included from src/bwa.cpp:39: +src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': +src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); + | ^~~~~~~~ +In file included from src/bwamem.h:47, + from src/fastmap.h:45, + from src/fastmap.cpp:42: +src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': +src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); + | ^~~~~~~~ +src/bwamem_pair.cpp: In function 'int mem_matesw_batch_pre(const mem_opt_t*, const bntseq_t*, const uint8_t*, const mem_pestat_t*, const mem_alnreg_t*, int, const uint8_t*, mem_alnreg_v*, mem_cache*, int, int32_t, int32_t&, int32_t&, int32_t)': +src/bwamem_pair.cpp:1028:33: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] + 1028 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufRefs in %s\n", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +src/bwamem_pair.cpp:1045:33: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] + 1045 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufQers in %s\n", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +src/bwamem_pair.cpp:1062:33: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] + 1062 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairs in %s\n", tid, __func__); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ar rcs libbwa.a src/fastmap.o src/bwtindex.o src/utils.o src/memcpy_bwamem.o src/kthread.o src/kstring.o src/ksw.o src/bntseq.o src/bwamem.o src/profiling.o src/bandedSWA.o src/FMI_search.o src/read_index_ele.o src/bwamem_pair.o src/kswv.o src/bwa.o src/bwamem_extra.o src/kopen.o g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now src/main.o libbwa.a -lpthread -lm -lz -L. -lbwa -Lext/safestringlib -lsafestring -o bwa-mem2.avx2 make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1' @@ -8092,22 +8128,7 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy32_s.o safeclib/memcpy32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmp_s.o safeclib/strcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strpbrk_s.o safeclib/strpbrk_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -In file included from src/kstring.cpp:28: -src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': -src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); - | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy_s.o safeclib/memcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldin_s.o safeclib/strcpyfldin_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strprefix_s.o safeclib/strprefix_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove16_s.o safeclib/memmove16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldout_s.o safeclib/strcpyfldout_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strremovews_s.o safeclib/strremovews_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove32_s.o safeclib/memmove32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfld_s.o safeclib/strcpyfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strspn_s.o safeclib/strspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove_s.o safeclib/memmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpy_s.o safeclib/strcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS In file included from src/utils.cpp:44: src/utils.cpp: In function 'pair64_t ks_ksmall_128(size_t, pair64_t*, size_t)': src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] @@ -8119,7 +8140,6 @@ src/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strstr_s.o safeclib/strstr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ @@ -8156,7 +8176,6 @@ src/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/mem_primitives_lib.o safeclib/mem_primitives_lib.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ @@ -8175,10 +8194,7 @@ src/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcspn_s.o safeclib/strcspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtok_s.o safeclib/strtok_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstchar_s.o safeclib/strfirstchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtolowercase_s.o safeclib/strtolowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldin_s.o safeclib/strcpyfldin_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/utils.cpp: In function 'uint64_t ks_ksmall_64(size_t, uint64_t*, size_t)': src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } @@ -8243,11 +8259,6 @@ src/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset16_s.o safeclib/memset16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstdiff_s.o safeclib/strfirstdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtouppercase_s.o safeclib/strtouppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset32_s.o safeclib/memset32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstsame_s.o safeclib/strfirstsame_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/utils.cpp: In function 'int ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)': src/kseq.h:135:109: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 135 | memcpy_bwamem(str->s + str->l, str->m - str->l, ks->buf + ks->begin, i - ks->begin, __FILE__, __LINE__); \ @@ -8261,10 +8272,31 @@ src/utils.cpp:50:1: note: in expansion of macro 'KSEQ_INIT2' 50 | KSEQ_INIT2(, gzFile, err_gzread) | ^~~~~~~~~~ -src/kopen.cpp: In function 'int ftp_open(const char*)': -src/kopen.cpp:257:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 257 | memcpy_bwamem(pasv_ip, 4 * sizeof(int), v, 4 * sizeof(int), __FILE__, __LINE__); - | ^~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strprefix_s.o safeclib/strprefix_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove16_s.o safeclib/memmove16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldout_s.o safeclib/strcpyfldout_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +In file included from src/kstring.cpp:28: +src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': +src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); + | ^~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strremovews_s.o safeclib/strremovews_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove32_s.o safeclib/memmove32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfld_s.o safeclib/strcpyfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strspn_s.o safeclib/strspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove_s.o safeclib/memmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpy_s.o safeclib/strcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strstr_s.o safeclib/strstr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/mem_primitives_lib.o safeclib/mem_primitives_lib.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcspn_s.o safeclib/strcspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtok_s.o safeclib/strtok_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstchar_s.o safeclib/strfirstchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtolowercase_s.o safeclib/strtolowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset16_s.o safeclib/memset16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstdiff_s.o safeclib/strfirstdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtouppercase_s.o safeclib/strtouppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset32_s.o safeclib/memset32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstsame_s.o safeclib/strfirstsame_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strzero_s.o safeclib/strzero_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset_s.o safeclib/memset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisalphanumeric_s.o safeclib/strisalphanumeric_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -8281,6 +8313,10 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strislowercase_s.o safeclib/strislowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsncpy_s.o safeclib/wcsncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/safe_mem_constraint.o safeclib/safe_mem_constraint.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +src/kopen.cpp: In function 'int ftp_open(const char*)': +src/kopen.cpp:257:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 257 | memcpy_bwamem(pasv_ip, 4 * sizeof(int), v, 4 * sizeof(int), __FILE__, __LINE__); + | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strismixedcase_s.o safeclib/strismixedcase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsnlen_s.o safeclib/wcsnlen_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strispassword_s.o safeclib/strispassword_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -8311,7 +8347,8 @@ | ~~~~~~~~~~~~~~~~~ ar rcs libsafestring.a obj/abort_handler_s.o obj/stpcpy_s.o obj/strlastsame_s.o obj/ignore_handler_s.o obj/stpncpy_s.o obj/strljustify_s.o obj/memcmp16_s.o obj/strcasecmp_s.o obj/strncat_s.o obj/memcmp32_s.o obj/strcasestr_s.o obj/strncpy_s.o obj/memcmp_s.o obj/strcat_s.o obj/strnlen_s.o obj/memcpy16_s.o obj/strcmpfld_s.o obj/strnterminate_s.o obj/memcpy32_s.o obj/strcmp_s.o obj/strpbrk_s.o obj/memcpy_s.o obj/strcpyfldin_s.o obj/strprefix_s.o obj/memmove16_s.o obj/strcpyfldout_s.o obj/strremovews_s.o obj/memmove32_s.o obj/strcpyfld_s.o obj/strspn_s.o obj/memmove_s.o obj/strcpy_s.o obj/strstr_s.o obj/mem_primitives_lib.o obj/strcspn_s.o obj/strtok_s.o obj/strfirstchar_s.o obj/strtolowercase_s.o obj/memset16_s.o obj/strfirstdiff_s.o obj/strtouppercase_s.o obj/memset32_s.o obj/strfirstsame_s.o obj/strzero_s.o obj/memset_s.o obj/strisalphanumeric_s.o obj/wcpcpy_s.o obj/memzero16_s.o obj/strisascii_s.o obj/wcscat_s.o obj/memzero32_s.o obj/strisdigit_s.o obj/wcscpy_s.o obj/memzero_s.o obj/strishex_s.o obj/wcsncat_s.o obj/strislowercase_s.o obj/wcsncpy_s.o obj/safe_mem_constraint.o obj/strismixedcase_s.o obj/wcsnlen_s.o obj/strispassword_s.o obj/wmemcmp_s.o obj/safe_str_constraint.o obj/strisuppercase_s.o obj/wmemcpy_s.o obj/strlastchar_s.o obj/wmemmove_s.o obj/snprintf_support.o obj/strlastdiff_s.o obj/wmemset_s.o make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' -In file included from src/bwamem_pair.cpp:36: +In file included from src/bwamem.h:47, + from src/bwamem_extra.cpp:33: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); @@ -8322,40 +8359,32 @@ src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ -In file included from src/bwa.cpp:39: +In file included from src/bwamem_pair.cpp:36: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ In file included from src/bwamem.h:47, - from src/bwamem.cpp:34: + from src/kthread.h:37, + from src/kthread.cpp:32: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ In file included from src/bwamem.h:47, - from src/bwamem_extra.cpp:33: + from src/bwamem.cpp:34: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ In file included from src/bwamem.h:47, - from src/kthread.h:37, - from src/kthread.cpp:32: + from src/fastmap.h:45, + from src/fastmap.cpp:42: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ -src/FMI_search.cpp: In member function 'int FMI_search::build_fm_index(const char*, char*, int64_t, int64_t*, int64_t*)': -src/FMI_search.cpp:278:28: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=] - 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); - | ~^ ~~~ - | | | - | int int64_t {aka long int} - | %ld -In file included from src/bwamem.h:47, - from src/fastmap.h:45, - from src/fastmap.cpp:42: +In file included from src/bwa.cpp:39: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); @@ -8847,16 +8876,6 @@ | | | | int int64_t {aka long int} | %ld -src/bwamem_pair.cpp: In function 'int mem_matesw_batch_pre(const mem_opt_t*, const bntseq_t*, const uint8_t*, const mem_pestat_t*, const mem_alnreg_t*, int, const uint8_t*, mem_alnreg_v*, mem_cache*, int, int32_t, int32_t&, int32_t&, int32_t)': -src/bwamem_pair.cpp:1028:33: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] - 1028 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufRefs in %s\n", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -src/bwamem_pair.cpp:1045:33: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] - 1045 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufQers in %s\n", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -src/bwamem_pair.cpp:1062:33: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] - 1062 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairs in %s\n", tid, __func__); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp: In function 'int mem_kernel1_core(FMI_search*, const mem_opt_t*, bseq1_t*, int, mem_chain_v*, mem_seed_t*, int64_t, mem_cache*, int)': src/bwamem.cpp:1006:25: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 1006 | fprintf(stderr, "[%0.4d] Re-allocating SMEM data structures due to enc_qdb\n", tid); @@ -8888,6 +8907,23 @@ src/bwamem.cpp:2374:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2374 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +src/FMI_search.cpp: In member function 'int FMI_search::build_fm_index(const char*, char*, int64_t, int64_t*, int64_t*)': +src/FMI_search.cpp:278:28: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=] + 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); + | ~^ ~~~ + | | | + | int int64_t {aka long int} + | %ld +src/bwamem_pair.cpp: In function 'int mem_matesw_batch_pre(const mem_opt_t*, const bntseq_t*, const uint8_t*, const mem_pestat_t*, const mem_alnreg_t*, int, const uint8_t*, mem_alnreg_v*, mem_cache*, int, int32_t, int32_t&, int32_t&, int32_t)': +src/bwamem_pair.cpp:1028:33: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] + 1028 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufRefs in %s\n", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +src/bwamem_pair.cpp:1045:33: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] + 1045 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufQers in %s\n", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +src/bwamem_pair.cpp:1062:33: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] + 1062 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairs in %s\n", tid, __func__); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ar rcs libbwa.a src/fastmap.o src/bwtindex.o src/utils.o src/memcpy_bwamem.o src/kthread.o src/kstring.o src/ksw.o src/bntseq.o src/bwamem.o src/profiling.o src/bandedSWA.o src/FMI_search.o src/read_index_ele.o src/bwamem_pair.o src/kswv.o src/bwa.o src/bwamem_extra.o src/kopen.o g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx512bw -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now src/main.o libbwa.a -lpthread -lm -lz -L. -lbwa -Lext/safestringlib -lsafestring -o bwa-mem2.avx512bw make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1' @@ -8933,12 +8969,14 @@ 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/1407575/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1407575/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/1063317 and its subdirectories -I: Current time: Wed Sep 3 13:16:38 -12 2025 -I: pbuilder-time-stamp: 1756948598 +I: removing directory /srv/workspace/pbuilder/1407575 and its subdirectories +I: Current time: Wed Oct 7 21:49:00 +14 2026 +I: pbuilder-time-stamp: 1791359340