Diff of the two buildlogs: -- --- b1/build.log 2025-04-18 12:04:31.693685537 +0000 +++ b2/build.log 2025-04-18 12:07:08.826353909 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu May 21 06:25:05 -12 2026 -I: pbuilder-time-stamp: 1779387905 +I: Current time: Sat Apr 19 02:04:35 +14 2025 +I: pbuilder-time-stamp: 1744977875 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -34,54 +34,86 @@ 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/123994/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/117029/tmp/hooks/D01_modify_environment starting +debug: Running on ionos2-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Apr 18 12:04 /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/117029/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/117029/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='i386' + 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]="i686-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=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=23 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='456469ec27a249278ab138dd8d76f31e' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='123994' - PS1='# ' - PS2='> ' + INVOCATION_ID=67843fb6990b4eac9026bf274972f882 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-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=117029 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.05bMNiFn/pbuilderrc_E1px --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.05bMNiFn/b1 --logfile b1/build.log bwa-mem2_2.2.1-1.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.05bMNiFn/pbuilderrc_X0MH --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.05bMNiFn/b2 --logfile b2/build.log bwa-mem2_2.2.1-1.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos16-i386 6.1.0-33-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.133-1 (2025-04-10) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-33-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.133-1 (2025-04-10) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/123994/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/117029/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -156,7 +188,7 @@ Get: 31 http://deb.debian.org/debian unstable/main i386 help2man i386 1.49.3 [198 kB] Get: 32 http://deb.debian.org/debian unstable/main i386 libsimde-dev all 0.8.2-3 [467 kB] Get: 33 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB] -Fetched 12.9 MB in 0s (71.4 MB/s) +Fetched 12.9 MB in 1s (11.7 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 ... 19827 files and directories currently installed.) @@ -303,7 +335,11 @@ 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/117029/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/117029/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 @@ -315,7 +351,7 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1' dh_auto_clean || true - make -j22 clean + make -j23 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 @@ -335,7 +371,7 @@ 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 -j22 "INSTALL=install --strip-program=true" EXE=bwa-mem2.sse2 ARCH_FLAGS=-msse2 + make -j23 "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' @@ -376,11 +412,15 @@ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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] @@ -419,6 +459,7 @@ 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/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 -Wformat -Werror=format-security -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; } | ^ @@ -492,7 +533,6 @@ 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/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 -Wformat -Werror=format-security -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; } | ^ @@ -511,7 +551,8 @@ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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__); \ @@ -525,20 +566,26 @@ 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/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 -Wformat -Werror=format-security -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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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); @@ -555,9 +602,14 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/bandedSWA.cpp: In member function 'int64_t BandedPairWiseSW::getTicks()': src/bandedSWA.cpp:106:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", @@ -610,27 +662,11 @@ | ~~~~~~~~~~ | | | int64_t {aka long long int} -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -638,27 +674,9 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/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/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 -Wformat -Werror=format-security -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: -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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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__); - | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -666,6 +684,12 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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: +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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -679,12 +703,27 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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__); + | ^~~~~~~~ +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 'void mem_pestat(const mem_opt_t*, int64_t, int, const mem_alnreg_v*, mem_pestat_t*)': src/bwamem_pair.cpp:103:105: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 103 | if (bwa_verbose >= 3) fprintf(stderr, "[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", isize[0].n, isize[1].n, isize[2].n, isize[3].n); @@ -710,7 +749,6 @@ | | | | long int size_t {aka unsigned int} | %d -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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", @@ -721,8 +759,6 @@ 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__); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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*)': @@ -742,6 +778,138 @@ 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/fastmap.cpp: In function 'ktp_data_t* kt_pipeline(void*, int, void*, mem_opt_t*, worker_t&)': +src/fastmap.cpp:217:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 217 | fprintf(stderr, "[0000] read_chunk: %ld, work_chunk_size: %ld, nseq: %d\n", + | ~~^ + | | + | long int + | %lld + 218 | aux->task_size, sz, ret->n_seqs); + | ~~~~~~~~~~~~~~ + | | + | int64_t {aka long long int} +src/fastmap.cpp:217:69: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 217 | fprintf(stderr, "[0000] read_chunk: %ld, work_chunk_size: %ld, nseq: %d\n", + | ~~^ + | | + | long int + | %lld + 218 | aux->task_size, sz, ret->n_seqs); + | ~~ + | | + | int64_t {aka long long int} +src/fastmap.cpp: In function 'int main_mem(int, char**)': +src/fastmap.cpp:895:49: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 895 | fprintf(stderr, "* Reference genome size: %ld bp\n", rlen); + | ~~^ ~~~~ + | | | + | long int int64_t {aka long long int} + | %lld +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:149:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 149 | printf("ref_seq_len = %ld\n", ref_seq_len); + | ~~^ ~~~~~~~~~~~ + | | | + | | int64_t {aka long long int} + | long int + | %lld +src/FMI_search.cpp:161:23: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); + | ~~^ ~~~~~~~~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:161:28: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); + | ~~^ ~~~~~~~~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:161:33: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); + | ~~^ ~~~~~~~~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:161:38: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); + | ~~^ ~~~~~~~~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:161:43: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); + | ~~^ ~~~~~~~~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:182:27: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 182 | printf("BWT[%ld] = 4\n", i); + | ~~^ ~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:199:55: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 199 | fprintf(stderr, "ERROR! i = %ld, c = %c\n", i, c); + | ~~^ ~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:209:31: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] + 209 | printf("sizeof CP_OCC = %ld\n", sizeof(CP_OCC)); + | ~~^ ~~~~~~~~~~~~~~ + | | | + | | unsigned int + | long int + | %d +src/FMI_search.cpp:278:28: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); + | ~^ ~~~ + | | | + | int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:278:48: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); + | ~~^ + | | + | long int + | %lld +src/FMI_search.cpp:302:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 302 | printf("max_occ_ind = %ld\n", i >> CP_SHIFT); + | ~~^ + | | + | long int + | %lld +src/FMI_search.cpp: In member function 'int FMI_search::build_index()': +src/FMI_search.cpp:365:38: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 365 | fprintf(stderr, "ref seq len = %ld\n", pac_len); + | ~~^ ~~~~~~~ + | | | + | | int64_t {aka long long int} + | long int + | %lld +src/FMI_search.cpp: In member function 'void FMI_search::load_index()': +src/FMI_search.cpp:423:59: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 423 | fprintf(stderr, "* Reference seq len for bi-index = %ld\n", reference_seq_len); + | ~~^ ~~~~~~~~~~~~~~~~~ + | | | + | | int64_t {aka long long int} + | long int + | %lld +src/FMI_search.cpp:462:42: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 462 | fprintf(stderr, "* sentinel-index: %ld\n", sentinel_index); + | ~~^ ~~~~~~~~~~~~~~ + | | | + | | int64_t {aka long long int} + | long int + | %lld +src/FMI_search.cpp:489:28: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 489 | fprintf(stderr, "%ld,\t%lu\n", x, (unsigned long)count[x]); + | ~~^ ~ + | | | + | long int int64_t {aka long long int} + | %lld 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] @@ -871,50 +1039,6 @@ 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:149:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 149 | printf("ref_seq_len = %ld\n", ref_seq_len); - | ~~^ ~~~~~~~~~~~ - | | | - | | int64_t {aka long long int} - | long int - | %lld -src/FMI_search.cpp:161:23: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); - | ~~^ ~~~~~~~~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:161:28: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); - | ~~^ ~~~~~~~~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:161:33: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); - | ~~^ ~~~~~~~~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:161:38: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); - | ~~^ ~~~~~~~~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:161:43: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); - | ~~^ ~~~~~~~~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:182:27: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 182 | printf("BWT[%ld] = 4\n", i); - | ~~^ ~ - | | | - | long int int64_t {aka long long int} - | %lld 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; } @@ -925,19 +1049,6 @@ src/bwamem.cpp:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ -src/FMI_search.cpp:199:55: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 199 | fprintf(stderr, "ERROR! i = %ld, c = %c\n", i, c); - | ~~^ ~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:209:31: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] - 209 | printf("sizeof CP_OCC = %ld\n", sizeof(CP_OCC)); - | ~~^ ~~~~~~~~~~~~~~ - | | | - | | unsigned int - | long int - | %d 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; } | ^ @@ -983,18 +1094,6 @@ src/bwamem.cpp:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ -src/FMI_search.cpp:278:28: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); - | ~^ ~~~ - | | | - | int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:278:48: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); - | ~~^ - | | - | long int - | %lld 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; } | ^ @@ -1004,41 +1103,6 @@ src/bwamem.cpp:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ -src/FMI_search.cpp:302:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 302 | printf("max_occ_ind = %ld\n", i >> CP_SHIFT); - | ~~^ - | | - | long int - | %lld -src/FMI_search.cpp: In member function 'int FMI_search::build_index()': -src/FMI_search.cpp:365:38: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 365 | fprintf(stderr, "ref seq len = %ld\n", pac_len); - | ~~^ ~~~~~~~ - | | | - | | int64_t {aka long long int} - | long int - | %lld -src/FMI_search.cpp: In member function 'void FMI_search::load_index()': -src/FMI_search.cpp:423:59: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 423 | fprintf(stderr, "* Reference seq len for bi-index = %ld\n", reference_seq_len); - | ~~^ ~~~~~~~~~~~~~~~~~ - | | | - | | int64_t {aka long long int} - | long int - | %lld -src/FMI_search.cpp:462:42: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 462 | fprintf(stderr, "* sentinel-index: %ld\n", sentinel_index); - | ~~^ ~~~~~~~~~~~~~~ - | | | - | | int64_t {aka long long int} - | long int - | %lld -src/FMI_search.cpp:489:28: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 489 | fprintf(stderr, "%ld,\t%lu\n", x, (unsigned long)count[x]); - | ~~^ ~ - | | | - | long int int64_t {aka long long int} - | %lld src/bwamem.cpp: In function 'mem_alnreg_t ks_ksmall_mem_ars2(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; } @@ -1299,27 +1363,6 @@ 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__); | ^~~~~~~~ -src/fastmap.cpp: In function 'ktp_data_t* kt_pipeline(void*, int, void*, mem_opt_t*, worker_t&)': -src/fastmap.cpp:217:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 217 | fprintf(stderr, "[0000] read_chunk: %ld, work_chunk_size: %ld, nseq: %d\n", - | ~~^ - | | - | long int - | %lld - 218 | aux->task_size, sz, ret->n_seqs); - | ~~~~~~~~~~~~~~ - | | - | int64_t {aka long long int} -src/fastmap.cpp:217:69: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 217 | fprintf(stderr, "[0000] read_chunk: %ld, work_chunk_size: %ld, nseq: %d\n", - | ~~^ - | | - | long int - | %lld - 218 | aux->task_size, sz, ret->n_seqs); - | ~~ - | | - | int64_t {aka long long int} 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); @@ -1375,13 +1418,6 @@ | ~~~~~~~~ | | | int64_t {aka long long int} -src/fastmap.cpp: In function 'int main_mem(int, char**)': -src/fastmap.cpp:895:49: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 895 | fprintf(stderr, "* Reference genome size: %ld bp\n", rlen); - | ~~^ ~~~~ - | | | - | long int int64_t {aka long long int} - | %lld 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); @@ -1496,11 +1532,14 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/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 -Wformat -Werror=format-security -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] @@ -1630,8 +1669,7 @@ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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__); \ @@ -1645,21 +1683,30 @@ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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); @@ -1676,14 +1723,14 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/bandedSWA.cpp: In member function 'int64_t BandedPairWiseSW::getTicks()': src/bandedSWA.cpp:106:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", @@ -1736,42 +1783,18 @@ | ~~~~~~~~~~ | | | int64_t {aka long long int} -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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: -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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/kthread.h:37, - from src/kthread.cpp:32: +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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -1783,16 +1806,23 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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__); - | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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: +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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -1801,11 +1831,18 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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: +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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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 src/bwamem_pair.cpp: In function 'void mem_pestat(const mem_opt_t*, int64_t, int, const mem_alnreg_v*, mem_pestat_t*)': src/bwamem_pair.cpp:103:105: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 103 | if (bwa_verbose >= 3) fprintf(stderr, "[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", isize[0].n, isize[1].n, isize[2].n, isize[3].n); @@ -1831,6 +1868,7 @@ | | | | long int size_t {aka unsigned int} | %d +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", @@ -1841,8 +1879,6 @@ 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__); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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*)': @@ -1855,6 +1891,145 @@ 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/fastmap.cpp: In function 'ktp_data_t* kt_pipeline(void*, int, void*, mem_opt_t*, worker_t&)': +src/fastmap.cpp:217:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 217 | fprintf(stderr, "[0000] read_chunk: %ld, work_chunk_size: %ld, nseq: %d\n", + | ~~^ + | | + | long int + | %lld + 218 | aux->task_size, sz, ret->n_seqs); + | ~~~~~~~~~~~~~~ + | | + | int64_t {aka long long int} +src/fastmap.cpp:217:69: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 217 | fprintf(stderr, "[0000] read_chunk: %ld, work_chunk_size: %ld, nseq: %d\n", + | ~~^ + | | + | long int + | %lld + 218 | aux->task_size, sz, ret->n_seqs); + | ~~ + | | + | int64_t {aka long long int} +src/fastmap.cpp: In function 'int main_mem(int, char**)': +src/fastmap.cpp:895:49: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 895 | fprintf(stderr, "* Reference genome size: %ld bp\n", rlen); + | ~~^ ~~~~ + | | | + | long int int64_t {aka long long int} + | %lld +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:149:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 149 | printf("ref_seq_len = %ld\n", ref_seq_len); + | ~~^ ~~~~~~~~~~~ + | | | + | | int64_t {aka long long int} + | long int + | %lld +src/FMI_search.cpp:161:23: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); + | ~~^ ~~~~~~~~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:161:28: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); + | ~~^ ~~~~~~~~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:161:33: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); + | ~~^ ~~~~~~~~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:161:38: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); + | ~~^ ~~~~~~~~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:161:43: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); + | ~~^ ~~~~~~~~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:182:27: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 182 | printf("BWT[%ld] = 4\n", i); + | ~~^ ~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:199:55: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 199 | fprintf(stderr, "ERROR! i = %ld, c = %c\n", i, c); + | ~~^ ~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:209:31: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] + 209 | printf("sizeof CP_OCC = %ld\n", sizeof(CP_OCC)); + | ~~^ ~~~~~~~~~~~~~~ + | | | + | | unsigned int + | long int + | %d +src/FMI_search.cpp:278:28: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); + | ~^ ~~~ + | | | + | int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:278:48: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); + | ~~^ + | | + | long int + | %lld +src/FMI_search.cpp:302:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 302 | printf("max_occ_ind = %ld\n", i >> CP_SHIFT); + | ~~^ + | | + | long int + | %lld +src/FMI_search.cpp: In member function 'int FMI_search::build_index()': +src/FMI_search.cpp:365:38: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 365 | fprintf(stderr, "ref seq len = %ld\n", pac_len); + | ~~^ ~~~~~~~ + | | | + | | int64_t {aka long long int} + | long int + | %lld +src/FMI_search.cpp: In member function 'void FMI_search::load_index()': +src/FMI_search.cpp:423:59: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 423 | fprintf(stderr, "* Reference seq len for bi-index = %ld\n", reference_seq_len); + | ~~^ ~~~~~~~~~~~~~~~~~ + | | | + | | int64_t {aka long long int} + | long int + | %lld +src/FMI_search.cpp:462:42: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 462 | fprintf(stderr, "* sentinel-index: %ld\n", sentinel_index); + | ~~^ ~~~~~~~~~~~~~~ + | | | + | | int64_t {aka long long int} + | long int + | %lld +src/FMI_search.cpp:489:28: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 489 | fprintf(stderr, "%ld,\t%lu\n", x, (unsigned long)count[x]); + | ~~^ ~ + | | | + | long int int64_t {aka long long int} + | %lld 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] @@ -2403,13 +2578,6 @@ | | | long int | %lld -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 'void mem_process_seqs(mem_opt_t*, int64_t, int, bseq1_t*, const mem_pestat_t*, worker_t&)': src/bwamem.cpp:1370:90: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 1370 | memcpy_bwamem(pes, 4 * sizeof(mem_pestat_t), pes0, 4 * sizeof(mem_pestat_t), __FILE__, __LINE__); // if pes0 != NULL, set the insert-size @@ -2443,138 +2611,6 @@ 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:149:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 149 | printf("ref_seq_len = %ld\n", ref_seq_len); - | ~~^ ~~~~~~~~~~~ - | | | - | | int64_t {aka long long int} - | long int - | %lld -src/FMI_search.cpp:161:23: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); - | ~~^ ~~~~~~~~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:161:28: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); - | ~~^ ~~~~~~~~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:161:33: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); - | ~~^ ~~~~~~~~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:161:38: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); - | ~~^ ~~~~~~~~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:161:43: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); - | ~~^ ~~~~~~~~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:182:27: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 182 | printf("BWT[%ld] = 4\n", i); - | ~~^ ~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:199:55: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 199 | fprintf(stderr, "ERROR! i = %ld, c = %c\n", i, c); - | ~~^ ~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:209:31: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] - 209 | printf("sizeof CP_OCC = %ld\n", sizeof(CP_OCC)); - | ~~^ ~~~~~~~~~~~~~~ - | | | - | | unsigned int - | long int - | %d -src/FMI_search.cpp:278:28: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); - | ~^ ~~~ - | | | - | int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:278:48: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); - | ~~^ - | | - | long int - | %lld -src/FMI_search.cpp:302:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 302 | printf("max_occ_ind = %ld\n", i >> CP_SHIFT); - | ~~^ - | | - | long int - | %lld -src/FMI_search.cpp: In member function 'int FMI_search::build_index()': -src/FMI_search.cpp:365:38: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 365 | fprintf(stderr, "ref seq len = %ld\n", pac_len); - | ~~^ ~~~~~~~ - | | | - | | int64_t {aka long long int} - | long int - | %lld -src/FMI_search.cpp: In member function 'void FMI_search::load_index()': -src/FMI_search.cpp:423:59: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 423 | fprintf(stderr, "* Reference seq len for bi-index = %ld\n", reference_seq_len); - | ~~^ ~~~~~~~~~~~~~~~~~ - | | | - | | int64_t {aka long long int} - | long int - | %lld -src/FMI_search.cpp:462:42: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 462 | fprintf(stderr, "* sentinel-index: %ld\n", sentinel_index); - | ~~^ ~~~~~~~~~~~~~~ - | | | - | | int64_t {aka long long int} - | long int - | %lld -src/FMI_search.cpp:489:28: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 489 | fprintf(stderr, "%ld,\t%lu\n", x, (unsigned long)count[x]); - | ~~^ ~ - | | | - | long int int64_t {aka long long int} - | %lld -src/fastmap.cpp: In function 'ktp_data_t* kt_pipeline(void*, int, void*, mem_opt_t*, worker_t&)': -src/fastmap.cpp:217:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 217 | fprintf(stderr, "[0000] read_chunk: %ld, work_chunk_size: %ld, nseq: %d\n", - | ~~^ - | | - | long int - | %lld - 218 | aux->task_size, sz, ret->n_seqs); - | ~~~~~~~~~~~~~~ - | | - | int64_t {aka long long int} -src/fastmap.cpp:217:69: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 217 | fprintf(stderr, "[0000] read_chunk: %ld, work_chunk_size: %ld, nseq: %d\n", - | ~~^ - | | - | long int - | %lld - 218 | aux->task_size, sz, ret->n_seqs); - | ~~ - | | - | int64_t {aka long long int} -src/fastmap.cpp: In function 'int main_mem(int, char**)': -src/fastmap.cpp:895:49: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 895 | fprintf(stderr, "* Reference genome size: %ld bp\n", rlen); - | ~~^ ~~~~ - | | | - | long int int64_t {aka long long int} - | %lld 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 -Wformat -Werror=format-security -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' @@ -2608,12 +2644,22 @@ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Isrc -Iext/safestringlib/include src/main.cpp -o src/main.o make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o +rm -f libsafestring.a +rm -f safestringtest +make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' +make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' +make[4]: Nothing to be done for 'directories'. +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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__); | ^~~~~~~~ -rm -f libsafestring.a +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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] @@ -2716,6 +2762,7 @@ 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/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 -Wformat -Werror=format-security -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; } | ^ @@ -2743,8 +2790,9 @@ src/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ -rm -f safestringtest -make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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__); \ @@ -2758,27 +2806,26 @@ src/utils.cpp:50:1: note: in expansion of macro 'KSEQ_INIT2' 50 | KSEQ_INIT2(, gzFile, err_gzread) | ^~~~~~~~~~ -make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' -make[4]: Nothing to be done for 'directories'. -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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); @@ -2795,7 +2842,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/bandedSWA.cpp: In member function 'int64_t BandedPairWiseSW::getTicks()': src/bandedSWA.cpp:106:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", @@ -2837,6 +2885,7 @@ | ~~~~~~~~~~ | | | int64_t {aka long long int} +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/bandedSWA.cpp:106:49: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", | ~~^ @@ -2848,24 +2897,6 @@ | ~~~~~~~~~~ | | | int64_t {aka long long int} -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -2875,9 +2906,7 @@ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/kthread.h:37, - from src/kthread.cpp:32: +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__); @@ -2885,32 +2914,33 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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__); - | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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: -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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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__); + | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -2919,7 +2949,19 @@ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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: +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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/bwamem_pair.cpp: In function 'void mem_pestat(const mem_opt_t*, int64_t, int, const mem_alnreg_v*, mem_pestat_t*)': src/bwamem_pair.cpp:103:105: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 103 | if (bwa_verbose >= 3) fprintf(stderr, "[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", isize[0].n, isize[1].n, isize[2].n, isize[3].n); @@ -2945,9 +2987,6 @@ | | | | long int size_t {aka unsigned int} | %d -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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", @@ -2958,9 +2997,6 @@ 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__); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/main.h:36, @@ -2970,8 +3006,7 @@ 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__); @@ -3080,40 +3115,6 @@ | | | | long int int64_t {aka long long int} | %lld -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/fastmap.cpp: In function 'ktp_data_t* kt_pipeline(void*, int, void*, mem_opt_t*, worker_t&)': -src/fastmap.cpp:217:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 217 | fprintf(stderr, "[0000] read_chunk: %ld, work_chunk_size: %ld, nseq: %d\n", - | ~~^ - | | - | long int - | %lld - 218 | aux->task_size, sz, ret->n_seqs); - | ~~~~~~~~~~~~~~ - | | - | int64_t {aka long long int} -src/fastmap.cpp:217:69: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 217 | fprintf(stderr, "[0000] read_chunk: %ld, work_chunk_size: %ld, nseq: %d\n", - | ~~^ - | | - | long int - | %lld - 218 | aux->task_size, sz, ret->n_seqs); - | ~~ - | | - | int64_t {aka long long int} -src/fastmap.cpp: In function 'int main_mem(int, char**)': -src/fastmap.cpp:895:49: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 895 | fprintf(stderr, "* Reference genome size: %ld bp\n", rlen); - | ~~^ ~~~~ - | | | - | long int int64_t {aka long long int} - | %lld 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] @@ -3662,6 +3663,13 @@ | | | long int | %lld +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 'void mem_process_seqs(mem_opt_t*, int64_t, int, bseq1_t*, const mem_pestat_t*, worker_t&)': src/bwamem.cpp:1370:90: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 1370 | memcpy_bwamem(pes, 4 * sizeof(mem_pestat_t), pes0, 4 * sizeof(mem_pestat_t), __FILE__, __LINE__); // if pes0 != NULL, set the insert-size @@ -3695,6 +3703,34 @@ 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/fastmap.cpp: In function 'ktp_data_t* kt_pipeline(void*, int, void*, mem_opt_t*, worker_t&)': +src/fastmap.cpp:217:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 217 | fprintf(stderr, "[0000] read_chunk: %ld, work_chunk_size: %ld, nseq: %d\n", + | ~~^ + | | + | long int + | %lld + 218 | aux->task_size, sz, ret->n_seqs); + | ~~~~~~~~~~~~~~ + | | + | int64_t {aka long long int} +src/fastmap.cpp:217:69: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 217 | fprintf(stderr, "[0000] read_chunk: %ld, work_chunk_size: %ld, nseq: %d\n", + | ~~^ + | | + | long int + | %lld + 218 | aux->task_size, sz, ret->n_seqs); + | ~~ + | | + | int64_t {aka long long int} +src/fastmap.cpp: In function 'int main_mem(int, char**)': +src/fastmap.cpp:895:49: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 895 | fprintf(stderr, "* Reference genome size: %ld bp\n", rlen); + | ~~^ ~~~~ + | | | + | long int int64_t {aka long long int} + | %lld 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 -Wformat -Werror=format-security -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' @@ -3722,20 +3758,14 @@ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Isrc -Iext/safestringlib/include src/bwamem_pair.cpp -o src/bwamem_pair.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Isrc -Iext/safestringlib/include src/kswv.cpp -o src/kswv.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Isrc -Iext/safestringlib/include src/bwa.cpp -o src/bwa.o -g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Isrc -Iext/safestringlib/include src/bwamem_extra.cpp -o src/bwamem_extra.o -g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Isrc -Iext/safestringlib/include src/kopen.cpp -o src/kopen.o -cd ext/safestringlib/ && make clean && make CC=gcc directories libsafestring.a -g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Isrc -Iext/safestringlib/include src/main.cpp -o src/main.o -make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' 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__); | ^~~~~~~~ -rm -f obj/*.o *~ core /*~ objtest/*.o -rm -f libsafestring.a -rm -f safestringtest -make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' +g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Isrc -Iext/safestringlib/include src/bwamem_extra.cpp -o src/bwamem_extra.o +g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Isrc -Iext/safestringlib/include src/kopen.cpp -o src/kopen.o +cd ext/safestringlib/ && make clean && make CC=gcc directories libsafestring.a 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] @@ -3801,10 +3831,6 @@ src/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ -make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' -make[4]: Nothing to be done for 'directories'. -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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; } @@ -3824,7 +3850,6 @@ 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/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 -Wformat -Werror=format-security -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; } | ^ @@ -3870,8 +3895,10 @@ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Isrc -Iext/safestringlib/include src/main.cpp -o src/main.o +make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' +rm -f obj/*.o *~ core /*~ objtest/*.o +rm -f libsafestring.a 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__); \ @@ -3885,13 +3912,22 @@ src/utils.cpp:50:1: note: in expansion of macro 'KSEQ_INIT2' 50 | KSEQ_INIT2(, gzFile, err_gzread) | ^~~~~~~~~~ +rm -f safestringtest +make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' +make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' +make[4]: Nothing to be done for 'directories'. +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -3903,6 +3939,7 @@ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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); @@ -3919,13 +3956,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/bandedSWA.cpp: In member function 'int64_t BandedPairWiseSW::getTicks()': src/bandedSWA.cpp:106:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", @@ -3978,28 +4008,40 @@ | ~~~~~~~~~~ | | | int64_t {aka long long int} +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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: +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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__); | ^~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -4011,15 +4053,14 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/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__); | ^~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -4027,23 +4068,10 @@ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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__); - | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/bwamem_pair.cpp: In function 'void mem_pestat(const mem_opt_t*, int64_t, int, const mem_alnreg_v*, mem_pestat_t*)': src/bwamem_pair.cpp:103:105: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 103 | if (bwa_verbose >= 3) fprintf(stderr, "[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", isize[0].n, isize[1].n, isize[2].n, isize[3].n); @@ -4057,6 +4085,7 @@ | | | | long int size_t {aka unsigned int} | %d +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/bwamem_pair.cpp:103:115: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 103 | if (bwa_verbose >= 3) fprintf(stderr, "[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", isize[0].n, isize[1].n, isize[2].n, isize[3].n); | ~~^ ~~~~~~~~~~ @@ -4069,136 +4098,46 @@ | | | | long int size_t {aka unsigned int} | %d +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS 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__); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/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.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:149:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 149 | printf("ref_seq_len = %ld\n", ref_seq_len); - | ~~^ ~~~~~~~~~~~ - | | | - | | int64_t {aka long long int} - | long int - | %lld -src/FMI_search.cpp:161:23: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); - | ~~^ ~~~~~~~~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:161:28: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); - | ~~^ ~~~~~~~~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:161:33: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); - | ~~^ ~~~~~~~~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:161:38: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); - | ~~^ ~~~~~~~~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:161:43: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); - | ~~^ ~~~~~~~~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:182:27: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 182 | printf("BWT[%ld] = 4\n", i); - | ~~^ ~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:199:55: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 199 | fprintf(stderr, "ERROR! i = %ld, c = %c\n", i, c); - | ~~^ ~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:209:31: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] - 209 | printf("sizeof CP_OCC = %ld\n", sizeof(CP_OCC)); - | ~~^ ~~~~~~~~~~~~~~ - | | | - | | unsigned int - | long int - | %d -src/FMI_search.cpp:278:28: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); - | ~^ ~~~ - | | | - | int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:278:48: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); - | ~~^ - | | - | long int - | %lld -src/FMI_search.cpp:302:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 302 | printf("max_occ_ind = %ld\n", i >> CP_SHIFT); - | ~~^ - | | - | long int - | %lld -src/FMI_search.cpp: In member function 'int FMI_search::build_index()': -src/FMI_search.cpp:365:38: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 365 | fprintf(stderr, "ref seq len = %ld\n", pac_len); - | ~~^ ~~~~~~~ - | | | - | | int64_t {aka long long int} - | long int - | %lld -src/FMI_search.cpp: In member function 'void FMI_search::load_index()': -src/FMI_search.cpp:423:59: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 423 | fprintf(stderr, "* Reference seq len for bi-index = %ld\n", reference_seq_len); - | ~~^ ~~~~~~~~~~~~~~~~~ - | | | - | | int64_t {aka long long int} - | long int - | %lld -src/FMI_search.cpp:462:42: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 462 | fprintf(stderr, "* sentinel-index: %ld\n", sentinel_index); - | ~~^ ~~~~~~~~~~~~~~ - | | | - | | int64_t {aka long long int} - | long int - | %lld -src/FMI_search.cpp:489:28: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 489 | fprintf(stderr, "%ld,\t%lu\n", x, (unsigned long)count[x]); - | ~~^ ~ - | | | - | long int int64_t {aka long long int} - | %lld +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] @@ -4707,6 +4646,27 @@ | ~~~~~~~~ | | | int64_t {aka long long int} +src/fastmap.cpp: In function 'ktp_data_t* kt_pipeline(void*, int, void*, mem_opt_t*, worker_t&)': +src/fastmap.cpp:217:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 217 | fprintf(stderr, "[0000] read_chunk: %ld, work_chunk_size: %ld, nseq: %d\n", + | ~~^ + | | + | long int + | %lld + 218 | aux->task_size, sz, ret->n_seqs); + | ~~~~~~~~~~~~~~ + | | + | int64_t {aka long long int} +src/fastmap.cpp:217:69: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 217 | fprintf(stderr, "[0000] read_chunk: %ld, work_chunk_size: %ld, nseq: %d\n", + | ~~^ + | | + | long int + | %lld + 218 | aux->task_size, sz, ret->n_seqs); + | ~~ + | | + | int64_t {aka long long int} 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); @@ -4757,6 +4717,13 @@ | | | | long int int64_t {aka long long int} | %lld +src/fastmap.cpp: In function 'int main_mem(int, char**)': +src/fastmap.cpp:895:49: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 895 | fprintf(stderr, "* Reference genome size: %ld bp\n", rlen); + | ~~^ ~~~~ + | | | + | long int int64_t {aka long long int} + | %lld src/bwamem.cpp: In function 'void* _mm_realloc(void*, int64_t, int64_t, int16_t)': src/bwamem.cpp:1842:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 1842 | memcpy_bwamem(nptr, nsize * dsize, ptr, csize, __FILE__, __LINE__); @@ -4780,41 +4747,110 @@ 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/fastmap.cpp: In function 'ktp_data_t* kt_pipeline(void*, int, void*, mem_opt_t*, worker_t&)': -src/fastmap.cpp:217:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 217 | fprintf(stderr, "[0000] read_chunk: %ld, work_chunk_size: %ld, nseq: %d\n", - | ~~^ - | | - | long int - | %lld - 218 | aux->task_size, sz, ret->n_seqs); - | ~~~~~~~~~~~~~~ - | | - | int64_t {aka long long int} -src/fastmap.cpp:217:69: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 217 | fprintf(stderr, "[0000] read_chunk: %ld, work_chunk_size: %ld, nseq: %d\n", - | ~~^ - | | - | long int - | %lld - 218 | aux->task_size, sz, ret->n_seqs); - | ~~ - | | - | int64_t {aka long long int} -src/fastmap.cpp: In function 'int main_mem(int, char**)': -src/fastmap.cpp:895:49: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 895 | fprintf(stderr, "* Reference genome size: %ld bp\n", rlen); - | ~~^ ~~~~ - | | | - | long int int64_t {aka long long int} - | %lld +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:149:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 149 | printf("ref_seq_len = %ld\n", ref_seq_len); + | ~~^ ~~~~~~~~~~~ + | | | + | | int64_t {aka long long int} + | long int + | %lld +src/FMI_search.cpp:161:23: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); + | ~~^ ~~~~~~~~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:161:28: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); + | ~~^ ~~~~~~~~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:161:33: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); + | ~~^ ~~~~~~~~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:161:38: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); + | ~~^ ~~~~~~~~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:161:43: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); + | ~~^ ~~~~~~~~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:182:27: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 182 | printf("BWT[%ld] = 4\n", i); + | ~~^ ~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:199:55: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 199 | fprintf(stderr, "ERROR! i = %ld, c = %c\n", i, c); + | ~~^ ~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:209:31: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] + 209 | printf("sizeof CP_OCC = %ld\n", sizeof(CP_OCC)); + | ~~^ ~~~~~~~~~~~~~~ + | | | + | | unsigned int + | long int + | %d +src/FMI_search.cpp:278:28: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); + | ~^ ~~~ + | | | + | int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:278:48: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); + | ~~^ + | | + | long int + | %lld +src/FMI_search.cpp:302:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 302 | printf("max_occ_ind = %ld\n", i >> CP_SHIFT); + | ~~^ + | | + | long int + | %lld +src/FMI_search.cpp: In member function 'int FMI_search::build_index()': +src/FMI_search.cpp:365:38: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 365 | fprintf(stderr, "ref seq len = %ld\n", pac_len); + | ~~^ ~~~~~~~ + | | | + | | int64_t {aka long long int} + | long int + | %lld +src/FMI_search.cpp: In member function 'void FMI_search::load_index()': +src/FMI_search.cpp:423:59: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 423 | fprintf(stderr, "* Reference seq len for bi-index = %ld\n", reference_seq_len); + | ~~^ ~~~~~~~~~~~~~~~~~ + | | | + | | int64_t {aka long long int} + | long int + | %lld +src/FMI_search.cpp:462:42: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 462 | fprintf(stderr, "* sentinel-index: %ld\n", sentinel_index); + | ~~^ ~~~~~~~~~~~~~~ + | | | + | | int64_t {aka long long int} + | long int + | %lld +src/FMI_search.cpp:489:28: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 489 | fprintf(stderr, "%ld,\t%lu\n", x, (unsigned long)count[x]); + | ~~^ ~ + | | | + | long int int64_t {aka long long int} + | %lld 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 -Wformat -Werror=format-security -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.avx2 make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1' @@ -4856,6 +4892,8 @@ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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] @@ -4926,7 +4964,11 @@ 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 -Wformat -Werror=format-security -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/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 -Wformat -Werror=format-security -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; } @@ -4991,12 +5033,8 @@ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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__); \ @@ -5010,8 +5048,6 @@ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -5019,6 +5055,14 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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); @@ -5035,12 +5079,15 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/bandedSWA.cpp: In member function 'int64_t BandedPairWiseSW::getTicks()': src/bandedSWA.cpp:106:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", @@ -5093,22 +5140,6 @@ | ~~~~~~~~~~ | | | int64_t {aka long long int} -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -5118,6 +5149,11 @@ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -5125,6 +5161,10 @@ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/kthread.h:37, from src/kthread.cpp:32: @@ -5132,17 +5172,13 @@ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/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__); | ^~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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: +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__); @@ -5157,15 +5193,6 @@ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/bwamem_pair.cpp: In function 'void mem_pestat(const mem_opt_t*, int64_t, int, const mem_alnreg_v*, mem_pestat_t*)': src/bwamem_pair.cpp:103:105: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 103 | if (bwa_verbose >= 3) fprintf(stderr, "[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", isize[0].n, isize[1].n, isize[2].n, isize[3].n); @@ -5191,6 +5218,8 @@ | | | | long int size_t {aka unsigned int} | %d +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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", @@ -5201,6 +5230,13 @@ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/main.h:36, @@ -5222,6 +5258,71 @@ 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] + 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } + | ^ +src/ksort.h:246:61: note: in expansion of macro 'KSORT_SWAP' + 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ + | ^~~~~~~~~~ +src/bwamem.cpp:47:1: note: in expansion of macro 'KSORT_INIT' + 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) + | ^~~~~~~~~~ +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; } + | ^ +src/ksort.h:250:53: note: in expansion of macro 'KSORT_SWAP' + 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ + | ^~~~~~~~~~ +src/bwamem.cpp:47:1: note: in expansion of macro 'KSORT_INIT' + 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) + | ^~~~~~~~~~ +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; } + | ^ +src/ksort.h:251:53: note: in expansion of macro 'KSORT_SWAP' + 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ + | ^~~~~~~~~~ +src/bwamem.cpp:47:1: note: in expansion of macro 'KSORT_INIT' + 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) + | ^~~~~~~~~~ +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; } + | ^ +src/ksort.h:252:52: note: in expansion of macro 'KSORT_SWAP' + 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ + | ^~~~~~~~~~ +src/bwamem.cpp:47:1: note: in expansion of macro 'KSORT_INIT' + 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) + | ^~~~~~~~~~ +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; } + | ^ +src/ksort.h:253:25: note: in expansion of macro 'KSORT_SWAP' + 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ + | ^~~~~~~~~~ +src/bwamem.cpp:47:1: note: in expansion of macro 'KSORT_INIT' + 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) + | ^~~~~~~~~~ +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; } + | ^ +src/ksort.h:259:33: note: in expansion of macro 'KSORT_SWAP' + 259 | KSORT_SWAP(type_t, *ll, *hh); \ + | ^~~~~~~~~~ +src/bwamem.cpp:47:1: note: in expansion of macro 'KSORT_INIT' + 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) + | ^~~~~~~~~~ +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; } + | ^ +src/ksort.h:261:25: note: in expansion of macro 'KSORT_SWAP' + 261 | KSORT_SWAP(type_t, *low, *hh); \ + | ^~~~~~~~~~ +src/bwamem.cpp:47:1: note: in expansion of macro 'KSORT_INIT' + 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) + | ^~~~~~~~~~ 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:149:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] 149 | printf("ref_seq_len = %ld\n", ref_seq_len); @@ -5313,6 +5414,16 @@ | | int64_t {aka long long int} | long int | %lld +src/bwamem.cpp: In function 'SMEM ks_ksmall_mem_intv1(size_t, SMEM*, 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; } + | ^ +src/ksort.h:246:61: note: in expansion of macro 'KSORT_SWAP' + 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ + | ^~~~~~~~~~ +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:462:42: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 462 | fprintf(stderr, "* sentinel-index: %ld\n", sentinel_index); | ~~^ ~~~~~~~~~~~~~~ @@ -5326,109 +5437,6 @@ | | | | long int int64_t {aka long long int} | %lld -src/fastmap.cpp: In function 'ktp_data_t* kt_pipeline(void*, int, void*, mem_opt_t*, worker_t&)': -src/fastmap.cpp:217:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 217 | fprintf(stderr, "[0000] read_chunk: %ld, work_chunk_size: %ld, nseq: %d\n", - | ~~^ - | | - | long int - | %lld - 218 | aux->task_size, sz, ret->n_seqs); - | ~~~~~~~~~~~~~~ - | | - | int64_t {aka long long int} -src/fastmap.cpp:217:69: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 217 | fprintf(stderr, "[0000] read_chunk: %ld, work_chunk_size: %ld, nseq: %d\n", - | ~~^ - | | - | long int - | %lld - 218 | aux->task_size, sz, ret->n_seqs); - | ~~ - | | - | int64_t {aka long long int} -src/fastmap.cpp: In function 'int main_mem(int, char**)': -src/fastmap.cpp:895:49: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 895 | fprintf(stderr, "* Reference genome size: %ld bp\n", rlen); - | ~~^ ~~~~ - | | | - | long int int64_t {aka long long int} - | %lld -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] - 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } - | ^ -src/ksort.h:246:61: note: in expansion of macro 'KSORT_SWAP' - 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ - | ^~~~~~~~~~ -src/bwamem.cpp:47:1: note: in expansion of macro 'KSORT_INIT' - 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) - | ^~~~~~~~~~ -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; } - | ^ -src/ksort.h:250:53: note: in expansion of macro 'KSORT_SWAP' - 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ - | ^~~~~~~~~~ -src/bwamem.cpp:47:1: note: in expansion of macro 'KSORT_INIT' - 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) - | ^~~~~~~~~~ -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; } - | ^ -src/ksort.h:251:53: note: in expansion of macro 'KSORT_SWAP' - 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ - | ^~~~~~~~~~ -src/bwamem.cpp:47:1: note: in expansion of macro 'KSORT_INIT' - 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) - | ^~~~~~~~~~ -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; } - | ^ -src/ksort.h:252:52: note: in expansion of macro 'KSORT_SWAP' - 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ - | ^~~~~~~~~~ -src/bwamem.cpp:47:1: note: in expansion of macro 'KSORT_INIT' - 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) - | ^~~~~~~~~~ -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; } - | ^ -src/ksort.h:253:25: note: in expansion of macro 'KSORT_SWAP' - 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ - | ^~~~~~~~~~ -src/bwamem.cpp:47:1: note: in expansion of macro 'KSORT_INIT' - 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) - | ^~~~~~~~~~ -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; } - | ^ -src/ksort.h:259:33: note: in expansion of macro 'KSORT_SWAP' - 259 | KSORT_SWAP(type_t, *ll, *hh); \ - | ^~~~~~~~~~ -src/bwamem.cpp:47:1: note: in expansion of macro 'KSORT_INIT' - 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) - | ^~~~~~~~~~ -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; } - | ^ -src/ksort.h:261:25: note: in expansion of macro 'KSORT_SWAP' - 261 | KSORT_SWAP(type_t, *low, *hh); \ - | ^~~~~~~~~~ -src/bwamem.cpp:47:1: note: in expansion of macro 'KSORT_INIT' - 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) - | ^~~~~~~~~~ -src/bwamem.cpp: In function 'SMEM ks_ksmall_mem_intv1(size_t, SMEM*, 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; } - | ^ -src/ksort.h:246:61: note: in expansion of macro 'KSORT_SWAP' - 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ - | ^~~~~~~~~~ -src/bwamem.cpp:49:1: note: in expansion of macro 'KSORT_INIT' - 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug - | ^~~~~~~~~~ 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; } | ^ @@ -5547,6 +5555,17 @@ src/bwamem.cpp:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ +src/fastmap.cpp: In function 'ktp_data_t* kt_pipeline(void*, int, void*, mem_opt_t*, worker_t&)': +src/fastmap.cpp:217:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 217 | fprintf(stderr, "[0000] read_chunk: %ld, work_chunk_size: %ld, nseq: %d\n", + | ~~^ + | | + | long int + | %lld + 218 | aux->task_size, sz, ret->n_seqs); + | ~~~~~~~~~~~~~~ + | | + | int64_t {aka long long int} src/bwamem.cpp: In function 'mem_alnreg_t ks_ksmall_mem_ars2(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; } @@ -5557,6 +5576,16 @@ src/bwamem.cpp:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ +src/fastmap.cpp:217:69: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 217 | fprintf(stderr, "[0000] read_chunk: %ld, work_chunk_size: %ld, nseq: %d\n", + | ~~^ + | | + | long int + | %lld + 218 | aux->task_size, sz, ret->n_seqs); + | ~~ + | | + | int64_t {aka long long int} 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; } | ^ @@ -5611,6 +5640,13 @@ src/bwamem.cpp:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ +src/fastmap.cpp: In function 'int main_mem(int, char**)': +src/fastmap.cpp:895:49: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 895 | fprintf(stderr, "* Reference genome size: %ld bp\n", rlen); + | ~~^ ~~~~ + | | | + | long int int64_t {aka long long int} + | %lld 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; } @@ -5941,7 +5977,7 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -j22 "INSTALL=install --strip-program=true" multi + make -j23 "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' @@ -5964,23 +6000,16 @@ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bandedSWA.cpp -o src/bandedSWA.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/FMI_search.cpp -o src/FMI_search.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/read_index_ele.cpp -o src/read_index_ele.o -g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem_pair.cpp -o src/bwamem_pair.o -g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kswv.cpp -o src/kswv.o -g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwa.cpp -o src/bwa.o -g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem_extra.cpp -o src/bwamem_extra.o -g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kopen.cpp -o src/kopen.o -cd ext/safestringlib/ && make clean && make CC=gcc directories libsafestring.a -g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/main.cpp -o src/main.o 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__); | ^~~~~~~~ -make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' -rm -f obj/*.o *~ core /*~ objtest/*.o -rm -f libsafestring.a -rm -f safestringtest -make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' +g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem_pair.cpp -o src/bwamem_pair.o +g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kswv.cpp -o src/kswv.o +g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwa.cpp -o src/bwa.o +g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem_extra.cpp -o src/bwamem_extra.o +g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kopen.cpp -o src/kopen.o 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] @@ -6046,6 +6075,7 @@ src/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ +cd ext/safestringlib/ && make clean && make CC=gcc directories libsafestring.a 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; } @@ -6110,9 +6140,10 @@ src/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ +g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/main.cpp -o src/main.o make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' -make[4]: Nothing to be done for 'directories'. -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +rm -f obj/*.o *~ core /*~ objtest/*.o +rm -f libsafestring.a 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__); \ @@ -6126,22 +6157,44 @@ src/utils.cpp:50:1: note: in expansion of macro 'KSEQ_INIT2' 50 | KSEQ_INIT2(, gzFile, err_gzread) | ^~~~~~~~~~ +rm -f safestringtest +make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' +make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' +make[4]: Nothing to be done for 'directories'. +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/bandedSWA.cpp: In member function 'int64_t BandedPairWiseSW::getTicks()': src/bandedSWA.cpp:106:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", @@ -6194,6 +6247,20 @@ | ~~~~~~~~~~ | | | int64_t {aka long long int} +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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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); @@ -6210,35 +6277,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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__); - | ^~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/kthread.h:37, from src/kthread.cpp:32: @@ -6246,20 +6285,6 @@ 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__); | ^~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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: -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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -6275,6 +6300,35 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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: +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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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__); + | ^~~~~~~~ +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 'void mem_pestat(const mem_opt_t*, int64_t, int, const mem_alnreg_v*, mem_pestat_t*)': src/bwamem_pair.cpp:103:105: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 103 | if (bwa_verbose >= 3) fprintf(stderr, "[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", isize[0].n, isize[1].n, isize[2].n, isize[3].n); @@ -6300,11 +6354,6 @@ | | | | long int size_t {aka unsigned int} | %d -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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", @@ -6315,19 +6364,6 @@ 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__); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/main.h:36, from src/main.cpp:35: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': @@ -6335,122 +6371,46 @@ 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__); | ^~~~~~~~ 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__); | ^~~~~~~~ -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:149:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 149 | printf("ref_seq_len = %ld\n", ref_seq_len); - | ~~^ ~~~~~~~~~~~ - | | | - | | int64_t {aka long long int} - | long int - | %lld -src/FMI_search.cpp:161:23: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); - | ~~^ ~~~~~~~~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:161:28: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); - | ~~^ ~~~~~~~~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:161:33: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); - | ~~^ ~~~~~~~~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:161:38: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); - | ~~^ ~~~~~~~~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:161:43: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); - | ~~^ ~~~~~~~~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:182:27: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 182 | printf("BWT[%ld] = 4\n", i); - | ~~^ ~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:199:55: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 199 | fprintf(stderr, "ERROR! i = %ld, c = %c\n", i, c); - | ~~^ ~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:209:31: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] - 209 | printf("sizeof CP_OCC = %ld\n", sizeof(CP_OCC)); - | ~~^ ~~~~~~~~~~~~~~ - | | | - | | unsigned int - | long int - | %d -src/FMI_search.cpp:278:28: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); - | ~^ ~~~ - | | | - | int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:278:48: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); - | ~~^ - | | - | long int - | %lld -src/FMI_search.cpp:302:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 302 | printf("max_occ_ind = %ld\n", i >> CP_SHIFT); - | ~~^ - | | - | long int - | %lld -src/FMI_search.cpp: In member function 'int FMI_search::build_index()': -src/FMI_search.cpp:365:38: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 365 | fprintf(stderr, "ref seq len = %ld\n", pac_len); - | ~~^ ~~~~~~~ - | | | - | | int64_t {aka long long int} - | long int - | %lld -src/FMI_search.cpp: In member function 'void FMI_search::load_index()': -src/FMI_search.cpp:423:59: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 423 | fprintf(stderr, "* Reference seq len for bi-index = %ld\n", reference_seq_len); - | ~~^ ~~~~~~~~~~~~~~~~~ - | | | - | | int64_t {aka long long int} - | long int - | %lld -src/FMI_search.cpp:462:42: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 462 | fprintf(stderr, "* sentinel-index: %ld\n", sentinel_index); - | ~~^ ~~~~~~~~~~~~~~ - | | | - | | int64_t {aka long long int} - | long int - | %lld -src/FMI_search.cpp:489:28: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 489 | fprintf(stderr, "%ld,\t%lu\n", x, (unsigned long)count[x]); - | ~~^ ~ - | | | - | long int int64_t {aka long long int} - | %lld +src/fastmap.cpp: In function 'ktp_data_t* kt_pipeline(void*, int, void*, mem_opt_t*, worker_t&)': +src/fastmap.cpp:217:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 217 | fprintf(stderr, "[0000] read_chunk: %ld, work_chunk_size: %ld, nseq: %d\n", + | ~~^ + | | + | long int + | %lld + 218 | aux->task_size, sz, ret->n_seqs); + | ~~~~~~~~~~~~~~ + | | + | int64_t {aka long long int} +src/fastmap.cpp:217:69: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 217 | fprintf(stderr, "[0000] read_chunk: %ld, work_chunk_size: %ld, nseq: %d\n", + | ~~^ + | | + | long int + | %lld + 218 | aux->task_size, sz, ret->n_seqs); + | ~~ + | | + | int64_t {aka long long int} +src/fastmap.cpp: In function 'int main_mem(int, char**)': +src/fastmap.cpp:895:49: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 895 | fprintf(stderr, "* Reference genome size: %ld bp\n", rlen); + | ~~^ ~~~~ + | | | + | long int int64_t {aka long long int} + | %lld 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] @@ -6708,27 +6668,6 @@ src/bwamem.cpp:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ -src/fastmap.cpp: In function 'ktp_data_t* kt_pipeline(void*, int, void*, mem_opt_t*, worker_t&)': -src/fastmap.cpp:217:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 217 | fprintf(stderr, "[0000] read_chunk: %ld, work_chunk_size: %ld, nseq: %d\n", - | ~~^ - | | - | long int - | %lld - 218 | aux->task_size, sz, ret->n_seqs); - | ~~~~~~~~~~~~~~ - | | - | int64_t {aka long long int} -src/fastmap.cpp:217:69: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 217 | fprintf(stderr, "[0000] read_chunk: %ld, work_chunk_size: %ld, nseq: %d\n", - | ~~^ - | | - | long int - | %lld - 218 | aux->task_size, sz, ret->n_seqs); - | ~~ - | | - | int64_t {aka long long int} 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; } @@ -6793,13 +6732,6 @@ src/bwamem.cpp:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ -src/fastmap.cpp: In function 'int main_mem(int, char**)': -src/fastmap.cpp:895:49: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 895 | fprintf(stderr, "* Reference genome size: %ld bp\n", rlen); - | ~~^ ~~~~ - | | | - | long int int64_t {aka long long int} - | %lld src/bwamem.cpp: In function 'mem_alnreg_t ks_ksmall_mem_ars_hash(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; } @@ -7027,16 +6959,120 @@ | | | long int | %lld +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:149:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 149 | printf("ref_seq_len = %ld\n", ref_seq_len); + | ~~^ ~~~~~~~~~~~ + | | | + | | int64_t {aka long long int} + | long int + | %lld +src/FMI_search.cpp:161:23: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); + | ~~^ ~~~~~~~~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:161:28: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); + | ~~^ ~~~~~~~~ + | | | + | long int int64_t {aka long long int} + | %lld src/bwamem.cpp: In function 'void mem_process_seqs(mem_opt_t*, int64_t, int, bseq1_t*, const mem_pestat_t*, worker_t&)': src/bwamem.cpp:1370:90: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 1370 | memcpy_bwamem(pes, 4 * sizeof(mem_pestat_t), pes0, 4 * sizeof(mem_pestat_t), __FILE__, __LINE__); // if pes0 != NULL, set the insert-size | ^~~~~~~~ +src/FMI_search.cpp:161:33: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); + | ~~^ ~~~~~~~~ + | | | + | long int int64_t {aka long long int} + | %lld src/bwamem.cpp:1374:31: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 1374 | "l_pac: %ld, n: %d\n", w.fmi->idx->bns->l_pac, n); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~ | | | | long int int64_t {aka long long int} | %lld +src/FMI_search.cpp:161:38: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); + | ~~^ ~~~~~~~~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:161:43: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); + | ~~^ ~~~~~~~~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:182:27: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 182 | printf("BWT[%ld] = 4\n", i); + | ~~^ ~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:199:55: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 199 | fprintf(stderr, "ERROR! i = %ld, c = %c\n", i, c); + | ~~^ ~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:209:31: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] + 209 | printf("sizeof CP_OCC = %ld\n", sizeof(CP_OCC)); + | ~~^ ~~~~~~~~~~~~~~ + | | | + | | unsigned int + | long int + | %d +src/FMI_search.cpp:278:28: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); + | ~^ ~~~ + | | | + | int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:278:48: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); + | ~~^ + | | + | long int + | %lld +src/FMI_search.cpp:302:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 302 | printf("max_occ_ind = %ld\n", i >> CP_SHIFT); + | ~~^ + | | + | long int + | %lld +src/FMI_search.cpp: In member function 'int FMI_search::build_index()': +src/FMI_search.cpp:365:38: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 365 | fprintf(stderr, "ref seq len = %ld\n", pac_len); + | ~~^ ~~~~~~~ + | | | + | | int64_t {aka long long int} + | long int + | %lld +src/FMI_search.cpp: In member function 'void FMI_search::load_index()': +src/FMI_search.cpp:423:59: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 423 | fprintf(stderr, "* Reference seq len for bi-index = %ld\n", reference_seq_len); + | ~~^ ~~~~~~~~~~~~~~~~~ + | | | + | | int64_t {aka long long int} + | long int + | %lld +src/FMI_search.cpp:462:42: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 462 | fprintf(stderr, "* sentinel-index: %ld\n", sentinel_index); + | ~~^ ~~~~~~~~~~~~~~ + | | | + | | int64_t {aka long long int} + | long int + | %lld +src/FMI_search.cpp:489:28: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 489 | fprintf(stderr, "%ld,\t%lu\n", x, (unsigned long)count[x]); + | ~~^ ~ + | | | + | long int int64_t {aka long long int} + | %lld src/bwamem.cpp: In function 'void* _mm_realloc(void*, int64_t, int64_t, int16_t)': src/bwamem.cpp:1842:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 1842 | memcpy_bwamem(nptr, nsize * dsize, ptr, csize, __FILE__, __LINE__); @@ -7084,29 +7120,6 @@ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bandedSWA.cpp -o src/bandedSWA.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/FMI_search.cpp -o src/FMI_search.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/read_index_ele.cpp -o src/read_index_ele.o -g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem_pair.cpp -o src/bwamem_pair.o -g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kswv.cpp -o src/kswv.o -g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwa.cpp -o src/bwa.o -g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem_extra.cpp -o src/bwamem_extra.o -g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kopen.cpp -o src/kopen.o -cd ext/safestringlib/ && make clean && make CC=gcc directories libsafestring.a -g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/main.cpp -o src/main.o -make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' -rm -f obj/*.o *~ core /*~ objtest/*.o -rm -f libsafestring.a -rm -f safestringtest -make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' -make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' -make[4]: Nothing to be done for 'directories'. -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/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 -Wformat -Werror=format-security -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] @@ -7236,7 +7249,7 @@ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem_pair.cpp -o src/bwamem_pair.o 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__); \ @@ -7250,13 +7263,36 @@ src/utils.cpp:50:1: note: in expansion of macro 'KSEQ_INIT2' 50 | KSEQ_INIT2(, gzFile, err_gzread) | ^~~~~~~~~~ +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__); + | ^~~~~~~~ +g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kswv.cpp -o src/kswv.o +g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwa.cpp -o src/bwa.o +g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem_extra.cpp -o src/bwamem_extra.o +g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kopen.cpp -o src/kopen.o +cd ext/safestringlib/ && make clean && make CC=gcc directories libsafestring.a +g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/main.cpp -o src/main.o +make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' +rm -f obj/*.o *~ core /*~ objtest/*.o +rm -f libsafestring.a +rm -f safestringtest +make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' +make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' +make[4]: Nothing to be done for 'directories'. +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -7266,28 +7302,16 @@ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/i386-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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/bandedSWA.cpp: In member function 'int64_t BandedPairWiseSW::getTicks()': src/bandedSWA.cpp:106:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", @@ -7340,16 +7364,23 @@ | ~~~~~~~~~~ | | | int64_t {aka long long int} -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/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 -Wformat -Werror=format-security -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/i386-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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -7364,31 +7395,23 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/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__); | ^~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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__); | ^~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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__); - | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -7400,17 +7423,26 @@ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/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/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 -Wformat -Werror=format-security -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: +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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/bwamem_pair.cpp: In function 'void mem_pestat(const mem_opt_t*, int64_t, int, const mem_alnreg_v*, mem_pestat_t*)': src/bwamem_pair.cpp:103:105: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 103 | if (bwa_verbose >= 3) fprintf(stderr, "[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", isize[0].n, isize[1].n, isize[2].n, isize[3].n); @@ -7436,6 +7468,8 @@ | | | | long int size_t {aka unsigned int} | %d +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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", @@ -7446,6 +7480,8 @@ 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__); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/main.h:36, @@ -7454,6 +7490,19 @@ 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/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__); + | ^~~~~~~~ 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:149:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] 149 | printf("ref_seq_len = %ld\n", ref_seq_len); @@ -7537,40 +7586,6 @@ | | int64_t {aka long long int} | long int | %lld -src/FMI_search.cpp: In member function 'void FMI_search::load_index()': -src/FMI_search.cpp:423:59: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 423 | fprintf(stderr, "* Reference seq len for bi-index = %ld\n", reference_seq_len); - | ~~^ ~~~~~~~~~~~~~~~~~ - | | | - | | int64_t {aka long long int} - | long int - | %lld -src/FMI_search.cpp:462:42: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 462 | fprintf(stderr, "* sentinel-index: %ld\n", sentinel_index); - | ~~^ ~~~~~~~~~~~~~~ - | | | - | | int64_t {aka long long int} - | long int - | %lld -src/FMI_search.cpp:489:28: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 489 | fprintf(stderr, "%ld,\t%lu\n", x, (unsigned long)count[x]); - | ~~^ ~ - | | | - | long int int64_t {aka long long int} - | %lld -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__); - | ^~~~~~~~ src/fastmap.cpp: In function 'ktp_data_t* kt_pipeline(void*, int, void*, mem_opt_t*, worker_t&)': src/fastmap.cpp:217:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 217 | fprintf(stderr, "[0000] read_chunk: %ld, work_chunk_size: %ld, nseq: %d\n", @@ -7592,6 +7607,27 @@ | ~~ | | | int64_t {aka long long int} +src/FMI_search.cpp: In member function 'void FMI_search::load_index()': +src/FMI_search.cpp:423:59: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 423 | fprintf(stderr, "* Reference seq len for bi-index = %ld\n", reference_seq_len); + | ~~^ ~~~~~~~~~~~~~~~~~ + | | | + | | int64_t {aka long long int} + | long int + | %lld +src/FMI_search.cpp:462:42: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 462 | fprintf(stderr, "* sentinel-index: %ld\n", sentinel_index); + | ~~^ ~~~~~~~~~~~~~~ + | | | + | | int64_t {aka long long int} + | long int + | %lld +src/FMI_search.cpp:489:28: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 489 | fprintf(stderr, "%ld,\t%lu\n", x, (unsigned long)count[x]); + | ~~^ ~ + | | | + | long int int64_t {aka long long int} + | %lld src/fastmap.cpp: In function 'int main_mem(int, char**)': src/fastmap.cpp:895:49: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 895 | fprintf(stderr, "* Reference genome size: %ld bp\n", rlen); @@ -8213,11 +8249,6 @@ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Isrc -Iext/safestringlib/include src/main.cpp -o src/main.o make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o -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__); - | ^~~~~~~~ rm -f libsafestring.a rm -f safestringtest make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' @@ -8227,7 +8258,13 @@ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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] @@ -8357,6 +8394,9 @@ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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__); \ @@ -8370,16 +8410,12 @@ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -8389,6 +8425,12 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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); @@ -8405,12 +8447,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -8430,11 +8466,6 @@ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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__); - | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -8461,6 +8492,30 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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__); + | ^~~~~~~~ +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__); + | ^~~~~~~~ +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/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__); + | ^~~~~~~~ src/bandedSWA.cpp: In member function 'int64_t BandedPairWiseSW::getTicks()': src/bandedSWA.cpp:106:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", @@ -8513,108 +8568,6 @@ | ~~~~~~~~~~ | | | int64_t {aka long long int} -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/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/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: -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__); - | ^~~~~~~~ -src/bwamem_pair.cpp: In function 'void mem_pestat(const mem_opt_t*, int64_t, int, const mem_alnreg_v*, mem_pestat_t*)': -src/bwamem_pair.cpp:103:105: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] - 103 | if (bwa_verbose >= 3) fprintf(stderr, "[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", isize[0].n, isize[1].n, isize[2].n, isize[3].n); - | ~~^ ~~~~~~~~~~ - | | | - | long int size_t {aka unsigned int} - | %d -src/bwamem_pair.cpp:103:110: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] - 103 | if (bwa_verbose >= 3) fprintf(stderr, "[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", isize[0].n, isize[1].n, isize[2].n, isize[3].n); - | ~~^ ~~~~~~~~~~ - | | | - | long int size_t {aka unsigned int} - | %d -src/bwamem_pair.cpp:103:115: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] - 103 | if (bwa_verbose >= 3) fprintf(stderr, "[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", isize[0].n, isize[1].n, isize[2].n, isize[3].n); - | ~~^ ~~~~~~~~~~ - | | | - | long int size_t {aka unsigned int} - | %d -src/bwamem_pair.cpp:103:120: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' {aka 'unsigned int'} [-Wformat=] - 103 | if (bwa_verbose >= 3) fprintf(stderr, "[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", isize[0].n, isize[1].n, isize[2].n, isize[3].n); - | ~~^ ~~~~~~~~~~ - | | | - | long int size_t {aka unsigned int} - | %d -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/fastmap.cpp: In function 'ktp_data_t* kt_pipeline(void*, int, void*, mem_opt_t*, worker_t&)': -src/fastmap.cpp:217:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 217 | fprintf(stderr, "[0000] read_chunk: %ld, work_chunk_size: %ld, nseq: %d\n", - | ~~^ - | | - | long int - | %lld - 218 | aux->task_size, sz, ret->n_seqs); - | ~~~~~~~~~~~~~~ - | | - | int64_t {aka long long int} -src/fastmap.cpp:217:69: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 217 | fprintf(stderr, "[0000] read_chunk: %ld, work_chunk_size: %ld, nseq: %d\n", - | ~~^ - | | - | long int - | %lld - 218 | aux->task_size, sz, ret->n_seqs); - | ~~ - | | - | int64_t {aka long long int} -src/fastmap.cpp: In function 'int main_mem(int, char**)': -src/fastmap.cpp:895:49: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 895 | fprintf(stderr, "* Reference genome size: %ld bp\n", rlen); - | ~~^ ~~~~ - | | | - | long int int64_t {aka long long int} - | %lld 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:149:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] 149 | printf("ref_seq_len = %ld\n", ref_seq_len); @@ -8678,6 +8631,12 @@ | | | | int int64_t {aka long long int} | %lld +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:278:48: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); | ~~^ @@ -8719,6 +8678,76 @@ | | | | long int int64_t {aka long long int} | %lld +src/bwamem_pair.cpp: In function 'void mem_pestat(const mem_opt_t*, int64_t, int, const mem_alnreg_v*, mem_pestat_t*)': +src/bwamem_pair.cpp:103:105: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] + 103 | if (bwa_verbose >= 3) fprintf(stderr, "[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", isize[0].n, isize[1].n, isize[2].n, isize[3].n); + | ~~^ ~~~~~~~~~~ + | | | + | long int size_t {aka unsigned int} + | %d +src/bwamem_pair.cpp:103:110: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] + 103 | if (bwa_verbose >= 3) fprintf(stderr, "[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", isize[0].n, isize[1].n, isize[2].n, isize[3].n); + | ~~^ ~~~~~~~~~~ + | | | + | long int size_t {aka unsigned int} + | %d +src/bwamem_pair.cpp:103:115: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] + 103 | if (bwa_verbose >= 3) fprintf(stderr, "[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", isize[0].n, isize[1].n, isize[2].n, isize[3].n); + | ~~^ ~~~~~~~~~~ + | | | + | long int size_t {aka unsigned int} + | %d +src/bwamem_pair.cpp:103:120: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' {aka 'unsigned int'} [-Wformat=] + 103 | if (bwa_verbose >= 3) fprintf(stderr, "[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", isize[0].n, isize[1].n, isize[2].n, isize[3].n); + | ~~^ ~~~~~~~~~~ + | | | + | long int size_t {aka unsigned int} + | %d +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: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/fastmap.cpp: In function 'ktp_data_t* kt_pipeline(void*, int, void*, mem_opt_t*, worker_t&)': +src/fastmap.cpp:217:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 217 | fprintf(stderr, "[0000] read_chunk: %ld, work_chunk_size: %ld, nseq: %d\n", + | ~~^ + | | + | long int + | %lld + 218 | aux->task_size, sz, ret->n_seqs); + | ~~~~~~~~~~~~~~ + | | + | int64_t {aka long long int} +src/fastmap.cpp:217:69: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 217 | fprintf(stderr, "[0000] read_chunk: %ld, work_chunk_size: %ld, nseq: %d\n", + | ~~^ + | | + | long int + | %lld + 218 | aux->task_size, sz, ret->n_seqs); + | ~~ + | | + | int64_t {aka long long int} +src/fastmap.cpp: In function 'int main_mem(int, char**)': +src/fastmap.cpp:895:49: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 895 | fprintf(stderr, "* Reference genome size: %ld bp\n", rlen); + | ~~^ ~~~~ + | | | + | long int int64_t {aka long long int} + | %lld 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] @@ -9300,6 +9329,13 @@ 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__); + | ^~~~~~~~ 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 -Wformat -Werror=format-security -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' @@ -9325,6 +9361,11 @@ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Isrc -Iext/safestringlib/include src/FMI_search.cpp -o src/FMI_search.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Isrc -Iext/safestringlib/include src/read_index_ele.cpp -o src/read_index_ele.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Isrc -Iext/safestringlib/include src/bwamem_pair.cpp -o src/bwamem_pair.o +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__); + | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Isrc -Iext/safestringlib/include src/kswv.cpp -o src/kswv.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Isrc -Iext/safestringlib/include src/bwa.cpp -o src/bwa.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Isrc -Iext/safestringlib/include src/bwamem_extra.cpp -o src/bwamem_extra.o @@ -9334,20 +9375,6 @@ make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a -rm -f safestringtest -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__); - | ^~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' -make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' -make[4]: Nothing to be done for 'directories'. -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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] @@ -9413,6 +9440,7 @@ src/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ +rm -f safestringtest 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; } @@ -9477,6 +9505,9 @@ src/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ +make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' +make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' +make[4]: Nothing to be done for 'directories'. 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__); \ @@ -9490,15 +9521,20 @@ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -9507,6 +9543,15 @@ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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); @@ -9523,15 +9568,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -9557,11 +9593,6 @@ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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__); - | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -9572,6 +9603,11 @@ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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__); + | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -9580,6 +9616,7 @@ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/bandedSWA.cpp: In member function 'int64_t BandedPairWiseSW::getTicks()': src/bandedSWA.cpp:106:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", @@ -9632,23 +9669,22 @@ | ~~~~~~~~~~ | | | int64_t {aka long long int} -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/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__); | ^~~~~~~~ -In file included from src/main.h:36, - from src/main.cpp:35: +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: +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__); @@ -9672,110 +9708,6 @@ 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:149:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 149 | printf("ref_seq_len = %ld\n", ref_seq_len); - | ~~^ ~~~~~~~~~~~ - | | | - | | int64_t {aka long long int} - | long int - | %lld -src/FMI_search.cpp:161:23: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); - | ~~^ ~~~~~~~~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:161:28: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); - | ~~^ ~~~~~~~~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:161:33: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); - | ~~^ ~~~~~~~~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:161:38: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); - | ~~^ ~~~~~~~~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:161:43: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); - | ~~^ ~~~~~~~~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:182:27: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 182 | printf("BWT[%ld] = 4\n", i); - | ~~^ ~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:199:55: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 199 | fprintf(stderr, "ERROR! i = %ld, c = %c\n", i, c); - | ~~^ ~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:209:31: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] - 209 | printf("sizeof CP_OCC = %ld\n", sizeof(CP_OCC)); - | ~~^ ~~~~~~~~~~~~~~ - | | | - | | unsigned int - | long int - | %d -src/FMI_search.cpp:278:28: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); - | ~^ ~~~ - | | | - | int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:278:48: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); - | ~~^ - | | - | long int - | %lld -src/FMI_search.cpp:302:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 302 | printf("max_occ_ind = %ld\n", i >> CP_SHIFT); - | ~~^ - | | - | long int - | %lld -src/FMI_search.cpp: In member function 'int FMI_search::build_index()': -src/FMI_search.cpp:365:38: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 365 | fprintf(stderr, "ref seq len = %ld\n", pac_len); - | ~~^ ~~~~~~~ - | | | - | | int64_t {aka long long int} - | long int - | %lld -src/FMI_search.cpp: In member function 'void FMI_search::load_index()': -src/FMI_search.cpp:423:59: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 423 | fprintf(stderr, "* Reference seq len for bi-index = %ld\n", reference_seq_len); - | ~~^ ~~~~~~~~~~~~~~~~~ - | | | - | | int64_t {aka long long int} - | long int - | %lld -src/FMI_search.cpp:462:42: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 462 | fprintf(stderr, "* sentinel-index: %ld\n", sentinel_index); - | ~~^ ~~~~~~~~~~~~~~ - | | | - | | int64_t {aka long long int} - | long int - | %lld -src/FMI_search.cpp:489:28: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 489 | fprintf(stderr, "%ld,\t%lu\n", x, (unsigned long)count[x]); - | ~~^ ~ - | | | - | long int int64_t {aka long long int} - | %lld src/bwamem_pair.cpp: In function 'void mem_pestat(const mem_opt_t*, int64_t, int, const mem_alnreg_v*, mem_pestat_t*)': src/bwamem_pair.cpp:103:105: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 103 | if (bwa_verbose >= 3) fprintf(stderr, "[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", isize[0].n, isize[1].n, isize[2].n, isize[3].n); @@ -9801,16 +9733,6 @@ | | | | long int size_t {aka unsigned int} | %d -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/fastmap.cpp: In function 'ktp_data_t* kt_pipeline(void*, int, void*, mem_opt_t*, worker_t&)': src/fastmap.cpp:217:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 217 | fprintf(stderr, "[0000] read_chunk: %ld, work_chunk_size: %ld, nseq: %d\n", @@ -9832,13 +9754,6 @@ | ~~ | | | int64_t {aka long long int} -src/fastmap.cpp: In function 'int main_mem(int, char**)': -src/fastmap.cpp:895:49: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 895 | fprintf(stderr, "* Reference genome size: %ld bp\n", rlen); - | ~~^ ~~~~ - | | | - | long int int64_t {aka long long int} - | %lld 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] @@ -9850,6 +9765,13 @@ src/bwamem.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ +src/fastmap.cpp: In function 'int main_mem(int, char**)': +src/fastmap.cpp:895:49: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 895 | fprintf(stderr, "* Reference genome size: %ld bp\n", rlen); + | ~~^ ~~~~ + | | | + | long int int64_t {aka long long int} + | %lld 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; } | ^ @@ -9904,6 +9826,16 @@ src/bwamem.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ +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 'SMEM ks_ksmall_mem_intv1(size_t, SMEM*, 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; } @@ -10326,6 +10258,14 @@ | | | | int int64_t {aka long long int} | %lld +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:149:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 149 | printf("ref_seq_len = %ld\n", ref_seq_len); + | ~~^ ~~~~~~~~~~~ + | | | + | | int64_t {aka long long int} + | long int + | %lld src/bwamem.cpp: In function 'void mem_chain_seeds(FMI_search*, const mem_opt_t*, const bntseq_t*, const bseq1_t*, int, int, mem_chain_v*, mem_seed_t*, int64_t, SMEM*, int64_t)': src/bwamem.cpp:912:46: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 912 | fprintf(stderr, "rbeg: %ld, slen: %d, cnt: %d, n: %d, m: %d, num_smem: %ld\n", @@ -10387,6 +10327,42 @@ | | | long int | %lld +src/FMI_search.cpp:161:23: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); + | ~~^ ~~~~~~~~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:161:28: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); + | ~~^ ~~~~~~~~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:161:33: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); + | ~~^ ~~~~~~~~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:161:38: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); + | ~~^ ~~~~~~~~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:161:43: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); + | ~~^ ~~~~~~~~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:182:27: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 182 | printf("BWT[%ld] = 4\n", i); + | ~~^ ~ + | | | + | long int int64_t {aka long long int} + | %lld src/bwamem.cpp: In function 'void mem_process_seqs(mem_opt_t*, int64_t, int, bseq1_t*, const mem_pestat_t*, worker_t&)': src/bwamem.cpp:1370:90: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 1370 | memcpy_bwamem(pes, 4 * sizeof(mem_pestat_t), pes0, 4 * sizeof(mem_pestat_t), __FILE__, __LINE__); // if pes0 != NULL, set the insert-size @@ -10397,10 +10373,70 @@ | | | | long int int64_t {aka long long int} | %lld +src/FMI_search.cpp:199:55: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 199 | fprintf(stderr, "ERROR! i = %ld, c = %c\n", i, c); + | ~~^ ~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:209:31: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] + 209 | printf("sizeof CP_OCC = %ld\n", sizeof(CP_OCC)); + | ~~^ ~~~~~~~~~~~~~~ + | | | + | | unsigned int + | long int + | %d +src/FMI_search.cpp:278:28: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); + | ~^ ~~~ + | | | + | int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:278:48: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); + | ~~^ + | | + | long int + | %lld +src/FMI_search.cpp:302:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 302 | printf("max_occ_ind = %ld\n", i >> CP_SHIFT); + | ~~^ + | | + | long int + | %lld +src/FMI_search.cpp: In member function 'int FMI_search::build_index()': +src/FMI_search.cpp:365:38: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 365 | fprintf(stderr, "ref seq len = %ld\n", pac_len); + | ~~^ ~~~~~~~ + | | | + | | int64_t {aka long long int} + | long int + | %lld +src/FMI_search.cpp: In member function 'void FMI_search::load_index()': +src/FMI_search.cpp:423:59: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 423 | fprintf(stderr, "* Reference seq len for bi-index = %ld\n", reference_seq_len); + | ~~^ ~~~~~~~~~~~~~~~~~ + | | | + | | int64_t {aka long long int} + | long int + | %lld +src/FMI_search.cpp:462:42: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 462 | fprintf(stderr, "* sentinel-index: %ld\n", sentinel_index); + | ~~^ ~~~~~~~~~~~~~~ + | | | + | | int64_t {aka long long int} + | long int + | %lld src/bwamem.cpp: In function 'void* _mm_realloc(void*, int64_t, int64_t, int16_t)': src/bwamem.cpp:1842:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 1842 | memcpy_bwamem(nptr, nsize * dsize, ptr, csize, __FILE__, __LINE__); | ^~~~~~~~ +src/FMI_search.cpp:489:28: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 489 | fprintf(stderr, "%ld,\t%lu\n", x, (unsigned long)count[x]); + | ~~^ ~ + | | | + | long int int64_t {aka long long int} + | %lld src/bwamem.cpp: In function 'void mem_chain2aln_across_reads_V2(const mem_opt_t*, const bntseq_t*, const uint8_t*, bseq1_t*, int, mem_chain_v*, mem_alnreg_v*, mem_cache*, uint8_t*, int)': src/bwamem.cpp:2237:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2237 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairArrays, in Left\n", tid); @@ -10459,13 +10495,17 @@ make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' make[4]: Nothing to be done for 'directories'. gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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] @@ -10531,6 +10571,7 @@ 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/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 -Wformat -Werror=format-security -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; } @@ -10595,11 +10636,8 @@ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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__); \ @@ -10613,16 +10651,26 @@ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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); @@ -10639,18 +10687,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS @@ -10691,16 +10727,18 @@ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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__); - | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 -Wformat -Werror=format-security -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: +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/bandedSWA.cpp: In member function 'int64_t BandedPairWiseSW::getTicks()': src/bandedSWA.cpp:106:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", @@ -10753,20 +10791,12 @@ | ~~~~~~~~~~ | | | int64_t {aka long long int} -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__); | ^~~~~~~~ -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/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] @@ -10785,145 +10815,12 @@ 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 'void mem_pestat(const mem_opt_t*, int64_t, int, const mem_alnreg_v*, mem_pestat_t*)': -src/bwamem_pair.cpp:103:105: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] - 103 | if (bwa_verbose >= 3) fprintf(stderr, "[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", isize[0].n, isize[1].n, isize[2].n, isize[3].n); - | ~~^ ~~~~~~~~~~ - | | | - | long int size_t {aka unsigned int} - | %d -src/bwamem_pair.cpp:103:110: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] - 103 | if (bwa_verbose >= 3) fprintf(stderr, "[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", isize[0].n, isize[1].n, isize[2].n, isize[3].n); - | ~~^ ~~~~~~~~~~ - | | | - | long int size_t {aka unsigned int} - | %d -src/bwamem_pair.cpp:103:115: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] - 103 | if (bwa_verbose >= 3) fprintf(stderr, "[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", isize[0].n, isize[1].n, isize[2].n, isize[3].n); - | ~~^ ~~~~~~~~~~ - | | | - | long int size_t {aka unsigned int} - | %d -src/bwamem_pair.cpp:103:120: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' {aka 'unsigned int'} [-Wformat=] - 103 | if (bwa_verbose >= 3) fprintf(stderr, "[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", isize[0].n, isize[1].n, isize[2].n, isize[3].n); - | ~~^ ~~~~~~~~~~ - | | | - | long int size_t {aka unsigned int} - | %d -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:149:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 149 | printf("ref_seq_len = %ld\n", ref_seq_len); - | ~~^ ~~~~~~~~~~~ - | | | - | | int64_t {aka long long int} - | long int - | %lld -src/FMI_search.cpp:161:23: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); - | ~~^ ~~~~~~~~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:161:28: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); - | ~~^ ~~~~~~~~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:161:33: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); - | ~~^ ~~~~~~~~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:161:38: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); - | ~~^ ~~~~~~~~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:161:43: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); - | ~~^ ~~~~~~~~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:182:27: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 182 | printf("BWT[%ld] = 4\n", i); - | ~~^ ~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:199:55: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 199 | fprintf(stderr, "ERROR! i = %ld, c = %c\n", i, c); - | ~~^ ~ - | | | - | long int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:209:31: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] - 209 | printf("sizeof CP_OCC = %ld\n", sizeof(CP_OCC)); - | ~~^ ~~~~~~~~~~~~~~ - | | | - | | unsigned int - | long int - | %d -src/FMI_search.cpp:278:28: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); - | ~^ ~~~ - | | | - | int int64_t {aka long long int} - | %lld -src/FMI_search.cpp:278:48: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); - | ~~^ - | | - | long int - | %lld -src/FMI_search.cpp:302:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 302 | printf("max_occ_ind = %ld\n", i >> CP_SHIFT); - | ~~^ - | | - | long int - | %lld -src/FMI_search.cpp: In member function 'int FMI_search::build_index()': -src/FMI_search.cpp:365:38: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 365 | fprintf(stderr, "ref seq len = %ld\n", pac_len); - | ~~^ ~~~~~~~ - | | | - | | int64_t {aka long long int} - | long int - | %lld -src/FMI_search.cpp: In member function 'void FMI_search::load_index()': -src/FMI_search.cpp:423:59: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 423 | fprintf(stderr, "* Reference seq len for bi-index = %ld\n", reference_seq_len); - | ~~^ ~~~~~~~~~~~~~~~~~ - | | | - | | int64_t {aka long long int} - | long int - | %lld -src/FMI_search.cpp:462:42: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 462 | fprintf(stderr, "* sentinel-index: %ld\n", sentinel_index); - | ~~^ ~~~~~~~~~~~~~~ - | | | - | | int64_t {aka long long int} - | long int - | %lld -src/FMI_search.cpp:489:28: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] - 489 | fprintf(stderr, "%ld,\t%lu\n", x, (unsigned long)count[x]); - | ~~^ ~ - | | | - | long int int64_t {aka long long int} - | %lld +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: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] @@ -11181,6 +11078,13 @@ src/bwamem.cpp:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ +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_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; } @@ -11482,10 +11386,114 @@ | | | | long int int64_t {aka long long int} | %lld +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:149:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 149 | printf("ref_seq_len = %ld\n", ref_seq_len); + | ~~^ ~~~~~~~~~~~ + | | | + | | int64_t {aka long long int} + | long int + | %lld +src/FMI_search.cpp:161:23: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); + | ~~^ ~~~~~~~~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:161:28: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); + | ~~^ ~~~~~~~~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:161:33: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); + | ~~^ ~~~~~~~~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:161:38: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); + | ~~^ ~~~~~~~~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:161:43: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 161 | printf("count = %ld, %ld, %ld, %ld, %ld\n", count[0], count[1], count[2], count[3], count[4]); + | ~~^ ~~~~~~~~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:182:27: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 182 | printf("BWT[%ld] = 4\n", i); + | ~~^ ~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:199:55: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 199 | fprintf(stderr, "ERROR! i = %ld, c = %c\n", i, c); + | ~~^ ~ + | | | + | long int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:209:31: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] + 209 | printf("sizeof CP_OCC = %ld\n", sizeof(CP_OCC)); + | ~~^ ~~~~~~~~~~~~~~ + | | | + | | unsigned int + | long int + | %d +src/FMI_search.cpp:278:28: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); + | ~^ ~~~ + | | | + | int int64_t {aka long long int} + | %lld +src/FMI_search.cpp:278:48: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); + | ~~^ + | | + | long int + | %lld +src/FMI_search.cpp:302:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 302 | printf("max_occ_ind = %ld\n", i >> CP_SHIFT); + | ~~^ + | | + | long int + | %lld +src/FMI_search.cpp: In member function 'int FMI_search::build_index()': +src/FMI_search.cpp:365:38: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 365 | fprintf(stderr, "ref seq len = %ld\n", pac_len); + | ~~^ ~~~~~~~ + | | | + | | int64_t {aka long long int} + | long int + | %lld +src/FMI_search.cpp: In member function 'void FMI_search::load_index()': +src/FMI_search.cpp:423:59: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 423 | fprintf(stderr, "* Reference seq len for bi-index = %ld\n", reference_seq_len); + | ~~^ ~~~~~~~~~~~~~~~~~ + | | | + | | int64_t {aka long long int} + | long int + | %lld src/bwamem.cpp: In function 'void* _mm_realloc(void*, int64_t, int64_t, int16_t)': src/bwamem.cpp:1842:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 1842 | memcpy_bwamem(nptr, nsize * dsize, ptr, csize, __FILE__, __LINE__); | ^~~~~~~~ +src/FMI_search.cpp:462:42: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 462 | fprintf(stderr, "* sentinel-index: %ld\n", sentinel_index); + | ~~^ ~~~~~~~~~~~~~~ + | | | + | | int64_t {aka long long int} + | long int + | %lld +src/FMI_search.cpp:489:28: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] + 489 | fprintf(stderr, "%ld,\t%lu\n", x, (unsigned long)count[x]); + | ~~^ ~ + | | | + | long int int64_t {aka long long int} + | %lld src/bwamem.cpp: In function 'void mem_chain2aln_across_reads_V2(const mem_opt_t*, const bntseq_t*, const uint8_t*, bseq1_t*, int, mem_chain_v*, mem_alnreg_v*, mem_cache*, uint8_t*, int)': src/bwamem.cpp:2237:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2237 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairArrays, in Left\n", tid); @@ -11505,13 +11513,6 @@ 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/fastmap.cpp: In function 'ktp_data_t* kt_pipeline(void*, int, void*, mem_opt_t*, worker_t&)': src/fastmap.cpp:217:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 217 | fprintf(stderr, "[0000] read_chunk: %ld, work_chunk_size: %ld, nseq: %d\n", @@ -11540,6 +11541,41 @@ | | | | long int int64_t {aka long long int} | %lld +src/bwamem_pair.cpp: In function 'void mem_pestat(const mem_opt_t*, int64_t, int, const mem_alnreg_v*, mem_pestat_t*)': +src/bwamem_pair.cpp:103:105: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] + 103 | if (bwa_verbose >= 3) fprintf(stderr, "[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", isize[0].n, isize[1].n, isize[2].n, isize[3].n); + | ~~^ ~~~~~~~~~~ + | | | + | long int size_t {aka unsigned int} + | %d +src/bwamem_pair.cpp:103:110: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] + 103 | if (bwa_verbose >= 3) fprintf(stderr, "[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", isize[0].n, isize[1].n, isize[2].n, isize[3].n); + | ~~^ ~~~~~~~~~~ + | | | + | long int size_t {aka unsigned int} + | %d +src/bwamem_pair.cpp:103:115: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] + 103 | if (bwa_verbose >= 3) fprintf(stderr, "[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", isize[0].n, isize[1].n, isize[2].n, isize[3].n); + | ~~^ ~~~~~~~~~~ + | | | + | long int size_t {aka unsigned int} + | %d +src/bwamem_pair.cpp:103:120: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' {aka 'unsigned int'} [-Wformat=] + 103 | if (bwa_verbose >= 3) fprintf(stderr, "[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", isize[0].n, isize[1].n, isize[2].n, isize[3].n); + | ~~^ ~~~~~~~~~~ + | | | + | long int size_t {aka unsigned int} + | %d +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 -Wformat -Werror=format-security -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' @@ -11576,8 +11612,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'bwa-mem2-dbgsym' in '../bwa-mem2-dbgsym_2.2.1-1_i386.deb'. dpkg-deb: building package 'bwa-mem2' in '../bwa-mem2_2.2.1-1_i386.deb'. +dpkg-deb: building package 'bwa-mem2-dbgsym' in '../bwa-mem2-dbgsym_2.2.1-1_i386.deb'. dpkg-genbuildinfo --build=binary -O../bwa-mem2_2.2.1-1_i386.buildinfo dpkg-genchanges --build=binary -O../bwa-mem2_2.2.1-1_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -11585,12 +11621,14 @@ 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/117029/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/117029/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/123994 and its subdirectories -I: Current time: Thu May 21 06:27:30 -12 2026 -I: pbuilder-time-stamp: 1779388050 +I: removing directory /srv/workspace/pbuilder/117029 and its subdirectories +I: Current time: Sat Apr 19 02:07:07 +14 2025 +I: pbuilder-time-stamp: 1744978027