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: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [bwa-mem2_2.2.1-1.dsc] I: copying [./bwa-mem2_2.2.1.orig.tar.xz] I: copying [./bwa-mem2_2.2.1-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./bwa-mem2_2.2.1-1.dsc: unsupported subcommand dpkg-source: info: extracting bwa-mem2 in bwa-mem2-2.2.1 dpkg-source: info: unpacking bwa-mem2_2.2.1.orig.tar.xz dpkg-source: info: unpacking bwa-mem2_2.2.1-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 0001-Fix-typo.patch dpkg-source: info: applying 0002-fixed-return-status-due-incorrect-input-files.patch dpkg-source: info: applying 0003-fixed-smem-memory-rellocation-issue-issue167.patch dpkg-source: info: applying 0004-Update-to-reflect-2.2.1-release-and-small-typo.patch dpkg-source: info: applying 0005-GCC-11-now-defines-__rdtsc-so-definition-test-condit.patch dpkg-source: info: applying 0006-fixed-segfault-due-to-memory-shortage-in-smem.patch dpkg-source: info: applying 0007-Merge-pull-request-229-from-gh-jphan-fix_n_processed.patch dpkg-source: info: applying hardening dpkg-source: info: applying simde 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: 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' 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='> ' 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' 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 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 -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), zlib1g-dev, libsimde-dev, help2man dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19827 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libsimde-dev; however: Package libsimde-dev is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libsimde-dev{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 33 newly installed, 0 to remove and 0 not upgraded. Need to get 12.9 MB of archives. After unpacking 53.2 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main i386 liblocale-gettext-perl i386 1.07-7+b1 [15.4 kB] Get: 2 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 3 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.46-5 [338 kB] Get: 4 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.46-5 [117 kB] Get: 5 http://deb.debian.org/debian unstable/main i386 file i386 1:5.46-5 [43.5 kB] Get: 6 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.23.1-1 [245 kB] Get: 7 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB] Get: 8 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-7 [1199 kB] Get: 9 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.41-4 [98.6 kB] Get: 10 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 11 http://deb.debian.org/debian unstable/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 12 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-7 [301 kB] Get: 13 http://deb.debian.org/debian unstable/main i386 autoconf all 2.72-3.1 [494 kB] Get: 14 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20240727.1 [60.2 kB] Get: 15 http://deb.debian.org/debian unstable/main i386 automake all 1:1.17-4 [862 kB] Get: 16 http://deb.debian.org/debian unstable/main i386 autopoint all 0.23.1-1 [770 kB] Get: 17 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 18 http://deb.debian.org/debian unstable/main i386 libtool all 2.5.4-4 [539 kB] Get: 19 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 22 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 23 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.192-4 [195 kB] Get: 24 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 25 http://deb.debian.org/debian unstable/main i386 libunistring5 i386 1.3-2 [471 kB] Get: 26 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.4 [732 kB] Get: 27 http://deb.debian.org/debian unstable/main i386 gettext i386 0.23.1-1 [1714 kB] Get: 28 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main i386 debhelper all 13.24.2 [919 kB] 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) 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.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-7+b1_i386.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.46-5_i386.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:i386. Preparing to unpack .../03-libmagic1t64_1%3a5.46-5_i386.deb ... Unpacking libmagic1t64:i386 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.46-5_i386.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.23.1-1_i386.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../06-libuchardet0_0.0.8-1+b2_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-7_i386.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.41-4_i386.deb ... Unpacking bsdextrautils (2.41-4) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../09-libpipeline1_1.5.8-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.13.0-1_i386.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-7_i386.deb ... Unpacking m4 (1.4.19-7) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.24.2_all.deb ... Unpacking libdebhelper-perl (13.24.2) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:i386. Preparing to unpack .../22-libelf1t64_0.192-4_i386.deb ... Unpacking libelf1t64:i386 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_i386.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:i386. Preparing to unpack .../24-libunistring5_1.3-2_i386.deb ... Unpacking libunistring5:i386 (1.3-2) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.4_i386.deb ... Unpacking libxml2:i386 (2.12.7+dfsg+really2.9.14-0.4) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.23.1-1_i386.deb ... Unpacking gettext (0.23.1-1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.24.2_all.deb ... Unpacking debhelper (13.24.2) ... Selecting previously unselected package help2man. Preparing to unpack .../30-help2man_1.49.3_i386.deb ... Unpacking help2man (1.49.3) ... Selecting previously unselected package libsimde-dev. Preparing to unpack .../31-libsimde-dev_0.8.2-3_all.deb ... Unpacking libsimde-dev (0.8.2-3) ... Selecting previously unselected package zlib1g-dev:i386. Preparing to unpack .../32-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_i386.deb ... Unpacking zlib1g-dev:i386 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libpipeline1:i386 (1.5.8-1) ... Setting up libsimde-dev (0.8.2-3) ... Setting up bsdextrautils (2.41-4) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libmagic1t64:i386 (1:5.46-5) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-7) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:i386 (0.192-4) ... Setting up autotools-dev (20240727.1) ... Setting up libunistring5:i386 (1.3-2) ... Setting up autopoint (0.23.1-1) ... Setting up autoconf (2.72-3.1) ... Setting up zlib1g-dev:i386 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:i386 (0.0.8-1+b2) ... Setting up libxml2:i386 (2.12.7+dfsg+really2.9.14-0.4) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-1) ... Setting up libtool (2.5.4-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.2) ... Processing triggers for libc-bin (2.41-7) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... 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 dpkg-buildpackage: info: source package bwa-mem2 dpkg-buildpackage: info: source version 2.2.1-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean 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[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 make[3]: 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[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' make[2]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1' make[1]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure 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[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' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' make arch=sse41 EXE=bwa-mem2.sse41 CXX=g++ all make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1' 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/fastmap.cpp -o src/fastmap.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/bwtindex.cpp -o src/bwtindex.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/utils.cpp -o src/utils.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/memcpy_bwamem.cpp -o src/memcpy_bwamem.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/kthread.cpp -o src/kthread.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/kstring.cpp -o src/kstring.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/ksw.cpp -o src/ksw.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/bntseq.cpp -o src/bntseq.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.cpp -o src/bwamem.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/profiling.cpp -o src/profiling.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/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 -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/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 -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/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 -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' 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' mkdir -p obj mkdir -p objtest gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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__); | ^~~~~~~~ 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] 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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ 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; } | ^ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/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; } | ^ src/ksort.h:259:33: note: in expansion of macro 'KSORT_SWAP' 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/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 src/utils.cpp: In function 'int ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)': src/kseq.h:135:109: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 135 | memcpy_bwamem(str->s + str->l, str->m - str->l, ks->buf + ks->begin, i - ks->begin, __FILE__, __LINE__); \ | ^~~~~~~~ src/kseq.h:159:9: note: in expansion of macro '__KS_GETUNTIL' 159 | __KS_GETUNTIL(__read, __bufsize) | ^~~~~~~~~~~~~ src/kseq.h:237:9: note: in expansion of macro 'KSTREAM_INIT' 237 | KSTREAM_INIT(type_t, __read, 16384) \ | ^~~~~~~~~~~~ src/utils.cpp:50:1: note: in expansion of macro 'KSEQ_INIT2' 50 | KSEQ_INIT2(, gzFile, err_gzread) | ^~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/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 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/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 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", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~~~~ | | | int64_t {aka long long int} src/bandedSWA.cpp:106:34: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~~~~ | | | int64_t {aka long long int} src/bandedSWA.cpp:106:39: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~ | | | int64_t {aka long long int} src/bandedSWA.cpp:106:44: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~~~~ | | | int64_t {aka long long int} 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", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, 108 | totalTicks); | ~~~~~~~~~~ | | | 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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 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.cpp:34: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ In file included from src/bwamem.h:47, from src/fastmap.h:45, from src/fastmap.cpp:42: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ In file included from src/bwamem.h:50: src/bwamem.cpp: In function 'bwtintv_t ks_ksmall_mem_intv(size_t, bwtintv_t*, size_t)': src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 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; } | ^ 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: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; } | ^ 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: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; } | ^ 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: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; } | ^ src/ksort.h:253:25: note: in expansion of macro 'KSORT_SWAP' 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ 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; } | ^ src/ksort.h:259:33: note: in expansion of macro 'KSORT_SWAP' 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ 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; } | ^ src/ksort.h:261:25: note: in expansion of macro 'KSORT_SWAP' 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ 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; } | ^ 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: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; } | ^ 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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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: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; } | ^ src/ksort.h:261:25: note: in expansion of macro 'KSORT_SWAP' 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ 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; } | ^ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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; } | ^ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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; } | ^ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/bwamem.cpp: In function 'mem_alnreg_t ks_ksmall_mem_ars_hash2(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; } | ^ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/bwamem.cpp: In function 'int test_and_merge(const mem_opt_t*, int64_t, mem_chain_t*, const mem_seed_t*, int, int)': 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:686:25: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 686 | fprintf(stderr, "[%0.4d] REA Re-allocating min_intv, query_pos, & rid\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:723:29: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 723 | fprintf(stderr, "[%0.4d] REA Re-allocating2 SMEM data structures due to enc_qdb\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:730:50: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long long int} | %lld src/bwamem.cpp:730:57: warning: format '%d' expects argument of type 'int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long long int} | %lld src/bwamem.cpp:765:59: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 765 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long long int} | %lld src/bwamem.cpp:765:66: warning: format '%d' expects argument of type 'int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 765 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long 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", | ~~^ | | | long int | %lld 913 | s.rbeg, s.len, cnt-1, p->n, p->m, num_smem); | ~~~~~~ | | | int64_t {aka long long int} src/bwamem.cpp:912:94: warning: format '%ld' expects argument of type 'long int', but argument 8 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", | ~~^ | | | long int | %lld 913 | s.rbeg, s.len, cnt-1, p->n, p->m, num_smem); | ~~~~~~~~ | | | 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:1048:51: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 1048 | fprintf(stderr, "Error [bug]: num_smem: %ld are more than allocated space %ld.\n", | ~~^ | | | long int | %lld 1049 | num_smem, *wsize_mem); | ~~~~~~~~ | | | int64_t {aka long long int} src/bwamem.cpp:1048:85: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 1048 | fprintf(stderr, "Error [bug]: num_smem: %ld are more than allocated space %ld.\n", | ~~^ | | | long int | %lld 1049 | num_smem, *wsize_mem); | ~~~~~~~~~~ | | | int64_t {aka long long int} In file included from src/bwa.h:38, from src/bwamem.h:36: src/bwamem.cpp:1052:18: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 1052 | printf_(VER, "6. Done! mem_collect_smem, num_smem: %ld\n", num_smem); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~ | | | int64_t {aka long long int} src/macro.h:39:41: note: in definition of macro 'printf_' 39 | fprintf(stderr, y); \ | ^ src/bwamem.cpp:1052:58: note: format string is defined here 1052 | printf_(VER, "6. Done! mem_collect_smem, num_smem: %ld\n", num_smem); | ~~^ | | | 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/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/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/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2260:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2260 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2280:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2280 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2333:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2333 | fprintf(stderr, "[0000] [%0.4d] Re-allocating seqPairArrays Right\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2358:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2358 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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.sse41 make[3]: Leaving 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' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' make arch=sse42 EXE=bwa-mem2.sse42 CXX=g++ all make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1' 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/fastmap.cpp -o src/fastmap.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/bwtindex.cpp -o src/bwtindex.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/utils.cpp -o src/utils.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/memcpy_bwamem.cpp -o src/memcpy_bwamem.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/kthread.cpp -o src/kthread.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/kstring.cpp -o src/kstring.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/ksw.cpp -o src/ksw.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/bntseq.cpp -o src/bntseq.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.cpp -o src/bwamem.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/profiling.cpp -o src/profiling.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/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 -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/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 -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/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 -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' 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__); | ^~~~~~~~ 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] 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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ 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; } | ^ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/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 src/utils.cpp: In function 'int ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)': src/kseq.h:135:109: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 135 | memcpy_bwamem(str->s + str->l, str->m - str->l, ks->buf + ks->begin, i - ks->begin, __FILE__, __LINE__); \ | ^~~~~~~~ src/kseq.h:159:9: note: in expansion of macro '__KS_GETUNTIL' 159 | __KS_GETUNTIL(__read, __bufsize) | ^~~~~~~~~~~~~ src/kseq.h:237:9: note: in expansion of macro 'KSTREAM_INIT' 237 | KSTREAM_INIT(type_t, __read, 16384) \ | ^~~~~~~~~~~~ src/utils.cpp:50:1: note: in expansion of macro 'KSEQ_INIT2' 50 | KSEQ_INIT2(, gzFile, err_gzread) | ^~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/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 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/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 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", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~~~~ | | | int64_t {aka long long int} src/bandedSWA.cpp:106:34: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~~~~ | | | int64_t {aka long long int} src/bandedSWA.cpp:106:39: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~ | | | int64_t {aka long long int} src/bandedSWA.cpp:106:44: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~~~~ | | | int64_t {aka long long int} 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", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, 108 | totalTicks); | ~~~~~~~~~~ | | | 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: 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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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); | ~~^ ~~~~~~~~~~ | | | | 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 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.cpp:34: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ In file included from src/bwamem.h:50: src/bwamem.cpp: In function 'bwtintv_t ks_ksmall_mem_intv(size_t, bwtintv_t*, size_t)': src/ksort.h:78:52: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 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; } | ^ 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: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; } | ^ 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: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; } | ^ 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: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; } | ^ src/ksort.h:253:25: note: in expansion of macro 'KSORT_SWAP' 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ 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; } | ^ src/ksort.h:259:33: note: in expansion of macro 'KSORT_SWAP' 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ 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; } | ^ src/ksort.h:261:25: note: in expansion of macro 'KSORT_SWAP' 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro 'KSORT_INIT' 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ 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; } | ^ 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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ 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; } | ^ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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; } | ^ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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; } | ^ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/bwamem.cpp: In function 'mem_alnreg_t ks_ksmall_mem_ars_hash2(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; } | ^ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/bwamem.cpp: In function 'int test_and_merge(const mem_opt_t*, int64_t, mem_chain_t*, const mem_seed_t*, int, int)': 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/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:686:25: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 686 | fprintf(stderr, "[%0.4d] REA Re-allocating min_intv, query_pos, & rid\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:723:29: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 723 | fprintf(stderr, "[%0.4d] REA Re-allocating2 SMEM data structures due to enc_qdb\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:730:50: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long long int} | %lld src/bwamem.cpp:730:57: warning: format '%d' expects argument of type 'int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long long int} | %lld src/bwamem.cpp:765:59: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 765 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long long int} | %lld src/bwamem.cpp:765:66: warning: format '%d' expects argument of type 'int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 765 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long 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", | ~~^ | | | long int | %lld 913 | s.rbeg, s.len, cnt-1, p->n, p->m, num_smem); | ~~~~~~ | | | int64_t {aka long long int} src/bwamem.cpp:912:94: warning: format '%ld' expects argument of type 'long int', but argument 8 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", | ~~^ | | | long int | %lld 913 | s.rbeg, s.len, cnt-1, p->n, p->m, num_smem); | ~~~~~~~~ | | | 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:1048:51: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 1048 | fprintf(stderr, "Error [bug]: num_smem: %ld are more than allocated space %ld.\n", | ~~^ | | | long int | %lld 1049 | num_smem, *wsize_mem); | ~~~~~~~~ | | | int64_t {aka long long int} src/bwamem.cpp:1048:85: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 1048 | fprintf(stderr, "Error [bug]: num_smem: %ld are more than allocated space %ld.\n", | ~~^ | | | long int | %lld 1049 | num_smem, *wsize_mem); | ~~~~~~~~~~ | | | int64_t {aka long long int} In file included from src/bwa.h:38, from src/bwamem.h:36: src/bwamem.cpp:1052:18: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 1052 | printf_(VER, "6. Done! mem_collect_smem, num_smem: %ld\n", num_smem); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~ | | | int64_t {aka long long int} src/macro.h:39:41: note: in definition of macro 'printf_' 39 | fprintf(stderr, y); \ | ^ src/bwamem.cpp:1052:58: note: format string is defined here 1052 | printf_(VER, "6. Done! mem_collect_smem, num_smem: %ld\n", num_smem); | ~~^ | | | 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 | ^~~~~~~~ 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/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/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2260:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2260 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2280:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2280 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2333:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2333 | fprintf(stderr, "[0000] [%0.4d] Re-allocating seqPairArrays Right\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2358:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2358 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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' 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' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' make arch=avx EXE=bwa-mem2.avx CXX=g++ all make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1' 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/fastmap.cpp -o src/fastmap.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/bwtindex.cpp -o src/bwtindex.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/utils.cpp -o src/utils.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/memcpy_bwamem.cpp -o src/memcpy_bwamem.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/kthread.cpp -o src/kthread.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/kstring.cpp -o src/kstring.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/ksw.cpp -o src/ksw.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/bntseq.cpp -o src/bntseq.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.cpp -o src/bwamem.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/profiling.cpp -o src/profiling.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/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 -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/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 -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/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 -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' 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 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] 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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ 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; } | ^ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/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' src/utils.cpp: In function 'int ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)': src/kseq.h:135:109: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 135 | memcpy_bwamem(str->s + str->l, str->m - str->l, ks->buf + ks->begin, i - ks->begin, __FILE__, __LINE__); \ | ^~~~~~~~ src/kseq.h:159:9: note: in expansion of macro '__KS_GETUNTIL' 159 | __KS_GETUNTIL(__read, __bufsize) | ^~~~~~~~~~~~~ src/kseq.h:237:9: note: in expansion of macro 'KSTREAM_INIT' 237 | KSTREAM_INIT(type_t, __read, 16384) \ | ^~~~~~~~~~~~ src/utils.cpp:50:1: note: in expansion of macro 'KSEQ_INIT2' 50 | KSEQ_INIT2(, gzFile, err_gzread) | ^~~~~~~~~~ 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 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/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 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", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~~~~ | | | int64_t {aka long long int} src/bandedSWA.cpp:106:34: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~~~~ | | | int64_t {aka long long int} src/bandedSWA.cpp:106:39: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~ | | | int64_t {aka long long int} src/bandedSWA.cpp:106:44: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~~~~ | | | int64_t {aka long long int} 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", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, 108 | totalTicks); | ~~~~~~~~~~ | | | 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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 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/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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/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__); | ^~~~~~~~ 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); | ~~^ ~~~~~~~~~~~ | | | | | 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.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] 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; } | ^ 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: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; } | ^ 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: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; } | ^ 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: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; } | ^ src/ksort.h:253:25: note: in expansion of macro 'KSORT_SWAP' 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ 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; } | ^ src/ksort.h:259:33: note: in expansion of macro 'KSORT_SWAP' 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ 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; } | ^ src/ksort.h:261:25: note: in expansion of macro 'KSORT_SWAP' 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro 'KSORT_INIT' 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ 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; } | ^ 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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ 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; } | ^ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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; } | ^ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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; } | ^ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/bwamem.cpp: In function 'mem_alnreg_t ks_ksmall_mem_ars_hash2(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; } | ^ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/bwamem.cpp: In function 'int test_and_merge(const mem_opt_t*, int64_t, mem_chain_t*, const mem_seed_t*, int, int)': 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/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:686:25: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 686 | fprintf(stderr, "[%0.4d] REA Re-allocating min_intv, query_pos, & rid\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:723:29: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 723 | fprintf(stderr, "[%0.4d] REA Re-allocating2 SMEM data structures due to enc_qdb\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:730:50: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long long int} | %lld src/bwamem.cpp:730:57: warning: format '%d' expects argument of type 'int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long long int} | %lld src/bwamem.cpp:765:59: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 765 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long long int} | %lld src/bwamem.cpp:765:66: warning: format '%d' expects argument of type 'int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 765 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long 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", | ~~^ | | | long int | %lld 913 | s.rbeg, s.len, cnt-1, p->n, p->m, num_smem); | ~~~~~~ | | | int64_t {aka long long int} src/bwamem.cpp:912:94: warning: format '%ld' expects argument of type 'long int', but argument 8 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", | ~~^ | | | long int | %lld 913 | s.rbeg, s.len, cnt-1, p->n, p->m, num_smem); | ~~~~~~~~ | | | 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:1048:51: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 1048 | fprintf(stderr, "Error [bug]: num_smem: %ld are more than allocated space %ld.\n", | ~~^ | | | long int | %lld 1049 | num_smem, *wsize_mem); | ~~~~~~~~ | | | int64_t {aka long long int} src/bwamem.cpp:1048:85: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 1048 | fprintf(stderr, "Error [bug]: num_smem: %ld are more than allocated space %ld.\n", | ~~^ | | | long int | %lld 1049 | num_smem, *wsize_mem); | ~~~~~~~~~~ | | | int64_t {aka long long int} In file included from src/bwa.h:38, from src/bwamem.h:36: src/bwamem.cpp:1052:18: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 1052 | printf_(VER, "6. Done! mem_collect_smem, num_smem: %ld\n", num_smem); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~ | | | int64_t {aka long long int} src/macro.h:39:41: note: in definition of macro 'printf_' 39 | fprintf(stderr, y); \ | ^ src/bwamem.cpp:1052:58: note: format string is defined here 1052 | printf_(VER, "6. Done! mem_collect_smem, num_smem: %ld\n", num_smem); | ~~^ | | | 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/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/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/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2260:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2260 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2280:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2280 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2333:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2333 | fprintf(stderr, "[0000] [%0.4d] Re-allocating seqPairArrays Right\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2358:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2358 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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' 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' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' make arch=avx2 EXE=bwa-mem2.avx2 CXX=g++ all make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1' 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/fastmap.cpp -o src/fastmap.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/bwtindex.cpp -o src/bwtindex.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/utils.cpp -o src/utils.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/memcpy_bwamem.cpp -o src/memcpy_bwamem.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/kthread.cpp -o src/kthread.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/kstring.cpp -o src/kstring.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/ksw.cpp -o src/ksw.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/bntseq.cpp -o src/bntseq.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.cpp -o src/bwamem.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/profiling.cpp -o src/profiling.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/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 -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/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 -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/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 -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' 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] 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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/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; } | ^ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/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; } | ^ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/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 src/utils.cpp: In function 'int ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)': src/kseq.h:135:109: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 135 | memcpy_bwamem(str->s + str->l, str->m - str->l, ks->buf + ks->begin, i - ks->begin, __FILE__, __LINE__); \ | ^~~~~~~~ src/kseq.h:159:9: note: in expansion of macro '__KS_GETUNTIL' 159 | __KS_GETUNTIL(__read, __bufsize) | ^~~~~~~~~~~~~ src/kseq.h:237:9: note: in expansion of macro 'KSTREAM_INIT' 237 | KSTREAM_INIT(type_t, __read, 16384) \ | ^~~~~~~~~~~~ src/utils.cpp:50:1: note: in expansion of macro 'KSEQ_INIT2' 50 | KSEQ_INIT2(, gzFile, err_gzread) | ^~~~~~~~~~ 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 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/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", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~~~~ | | | int64_t {aka long long int} src/bandedSWA.cpp:106:34: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~~~~ | | | int64_t {aka long long int} src/bandedSWA.cpp:106:39: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~ | | | int64_t {aka long long int} src/bandedSWA.cpp:106:44: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~~~~ | | | int64_t {aka long long int} 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", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, 108 | totalTicks); | ~~~~~~~~~~ | | | 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/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: 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/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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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); | ~~^ ~~~~~~~~~~ | | | | 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", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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/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/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: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; } | ^ 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: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; } | ^ 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: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; } | ^ 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: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; } | ^ src/ksort.h:253:25: note: in expansion of macro 'KSORT_SWAP' 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ 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; } | ^ src/ksort.h:259:33: note: in expansion of macro 'KSORT_SWAP' 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ 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; } | ^ src/ksort.h:261:25: note: in expansion of macro 'KSORT_SWAP' 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro 'KSORT_INIT' 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ 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; } | ^ 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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ 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; } | ^ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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; } | ^ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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; } | ^ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/bwamem.cpp: In function 'mem_alnreg_t ks_ksmall_mem_ars_hash2(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; } | ^ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/bwamem.cpp: In function 'int test_and_merge(const mem_opt_t*, int64_t, mem_chain_t*, const mem_seed_t*, int, int)': 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/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:686:25: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 686 | fprintf(stderr, "[%0.4d] REA Re-allocating min_intv, query_pos, & rid\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:723:29: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 723 | fprintf(stderr, "[%0.4d] REA Re-allocating2 SMEM data structures due to enc_qdb\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:730:50: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long long int} | %lld src/bwamem.cpp:730:57: warning: format '%d' expects argument of type 'int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long long int} | %lld src/bwamem.cpp:765:59: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 765 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long long int} | %lld src/bwamem.cpp:765:66: warning: format '%d' expects argument of type 'int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 765 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long 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", | ~~^ | | | long int | %lld 913 | s.rbeg, s.len, cnt-1, p->n, p->m, num_smem); | ~~~~~~ | | | int64_t {aka long long int} src/bwamem.cpp:912:94: warning: format '%ld' expects argument of type 'long int', but argument 8 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", | ~~^ | | | long int | %lld 913 | s.rbeg, s.len, cnt-1, p->n, p->m, num_smem); | ~~~~~~~~ | | | 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:1048:51: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 1048 | fprintf(stderr, "Error [bug]: num_smem: %ld are more than allocated space %ld.\n", | ~~^ | | | long int | %lld 1049 | num_smem, *wsize_mem); | ~~~~~~~~ | | | int64_t {aka long long int} src/bwamem.cpp:1048:85: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 1048 | fprintf(stderr, "Error [bug]: num_smem: %ld are more than allocated space %ld.\n", | ~~^ | | | long int | %lld 1049 | num_smem, *wsize_mem); | ~~~~~~~~~~ | | | int64_t {aka long long int} In file included from src/bwa.h:38, from src/bwamem.h:36: src/bwamem.cpp:1052:18: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 1052 | printf_(VER, "6. Done! mem_collect_smem, num_smem: %ld\n", num_smem); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~ | | | int64_t {aka long long int} src/macro.h:39:41: note: in definition of macro 'printf_' 39 | fprintf(stderr, y); \ | ^ src/bwamem.cpp:1052:58: note: format string is defined here 1052 | printf_(VER, "6. Done! mem_collect_smem, num_smem: %ld\n", num_smem); | ~~^ | | | 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/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/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/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2260:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2260 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2280:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2280 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2333:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2333 | fprintf(stderr, "[0000] [%0.4d] Re-allocating seqPairArrays Right\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2358:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2358 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 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' 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' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' make arch=avx512 EXE=bwa-mem2.avx512bw CXX=g++ all make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1' 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/fastmap.cpp -o src/fastmap.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/bwtindex.cpp -o src/bwtindex.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/utils.cpp -o src/utils.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/memcpy_bwamem.cpp -o src/memcpy_bwamem.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/kthread.cpp -o src/kthread.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/kstring.cpp -o src/kstring.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/ksw.cpp -o src/ksw.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/bntseq.cpp -o src/bntseq.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.cpp -o src/bwamem.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/profiling.cpp -o src/profiling.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/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 -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/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 -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/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 -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' 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__); | ^~~~~~~~ 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] 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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/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/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; } | ^ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/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__); | ^~~~~~~~ src/utils.cpp: In function 'int ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)': src/kseq.h:135:109: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 135 | memcpy_bwamem(str->s + str->l, str->m - str->l, ks->buf + ks->begin, i - ks->begin, __FILE__, __LINE__); \ | ^~~~~~~~ src/kseq.h:159:9: note: in expansion of macro '__KS_GETUNTIL' 159 | __KS_GETUNTIL(__read, __bufsize) | ^~~~~~~~~~~~~ src/kseq.h:237:9: note: in expansion of macro 'KSTREAM_INIT' 237 | KSTREAM_INIT(type_t, __read, 16384) \ | ^~~~~~~~~~~~ src/utils.cpp:50:1: note: in expansion of macro 'KSEQ_INIT2' 50 | KSEQ_INIT2(, gzFile, err_gzread) | ^~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/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 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/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 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", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~~~~ | | | int64_t {aka long long int} src/bandedSWA.cpp:106:34: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~~~~ | | | int64_t {aka long long int} src/bandedSWA.cpp:106:39: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~ | | | int64_t {aka long long int} src/bandedSWA.cpp:106:44: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~~~~ | | | int64_t {aka long long int} 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", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, 108 | totalTicks); | ~~~~~~~~~~ | | | 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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 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/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: 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: 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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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); | ~~^ ~~~~~~~~~~ | | | | 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 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.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); | ~~^ ~~~~~~~~~~~ | | | | | 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] 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; } | ^ 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: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; } | ^ 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: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; } | ^ 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: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; } | ^ src/ksort.h:253:25: note: in expansion of macro 'KSORT_SWAP' 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ 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; } | ^ src/ksort.h:259:33: note: in expansion of macro 'KSORT_SWAP' 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ 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; } | ^ src/ksort.h:261:25: note: in expansion of macro 'KSORT_SWAP' 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro 'KSORT_INIT' 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ 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; } | ^ 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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ 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; } | ^ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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; } | ^ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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; } | ^ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/bwamem.cpp: In function 'mem_alnreg_t ks_ksmall_mem_ars_hash2(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; } | ^ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/bwamem.cpp: In function 'int test_and_merge(const mem_opt_t*, int64_t, mem_chain_t*, const mem_seed_t*, int, int)': 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/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:686:25: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 686 | fprintf(stderr, "[%0.4d] REA Re-allocating min_intv, query_pos, & rid\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:723:29: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 723 | fprintf(stderr, "[%0.4d] REA Re-allocating2 SMEM data structures due to enc_qdb\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:730:50: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long long int} | %lld src/bwamem.cpp:730:57: warning: format '%d' expects argument of type 'int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long long int} | %lld src/bwamem.cpp:765:59: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 765 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long long int} | %lld src/bwamem.cpp:765:66: warning: format '%d' expects argument of type 'int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 765 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long 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", | ~~^ | | | long int | %lld 913 | s.rbeg, s.len, cnt-1, p->n, p->m, num_smem); | ~~~~~~ | | | int64_t {aka long long int} src/bwamem.cpp:912:94: warning: format '%ld' expects argument of type 'long int', but argument 8 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", | ~~^ | | | long int | %lld 913 | s.rbeg, s.len, cnt-1, p->n, p->m, num_smem); | ~~~~~~~~ | | | 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:1048:51: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 1048 | fprintf(stderr, "Error [bug]: num_smem: %ld are more than allocated space %ld.\n", | ~~^ | | | long int | %lld 1049 | num_smem, *wsize_mem); | ~~~~~~~~ | | | int64_t {aka long long int} src/bwamem.cpp:1048:85: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 1048 | fprintf(stderr, "Error [bug]: num_smem: %ld are more than allocated space %ld.\n", | ~~^ | | | long int | %lld 1049 | num_smem, *wsize_mem); | ~~~~~~~~~~ | | | int64_t {aka long long int} In file included from src/bwa.h:38, from src/bwamem.h:36: src/bwamem.cpp:1052:18: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 1052 | printf_(VER, "6. Done! mem_collect_smem, num_smem: %ld\n", num_smem); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~ | | | int64_t {aka long long int} src/macro.h:39:41: note: in definition of macro 'printf_' 39 | fprintf(stderr, y); \ | ^ src/bwamem.cpp:1052:58: note: format string is defined here 1052 | printf_(VER, "6. Done! mem_collect_smem, num_smem: %ld\n", num_smem); | ~~^ | | | 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/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/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/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2260:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2260 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2280:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2280 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2333:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2333 | fprintf(stderr, "[0000] [%0.4d] Re-allocating seqPairArrays Right\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2358:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2358 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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.avx512bw make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -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[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' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' make arch=sse41 EXE=bwa-mem2.sse41 CXX=g++ all make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1' 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/fastmap.cpp -o src/fastmap.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/bwtindex.cpp -o src/bwtindex.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/utils.cpp -o src/utils.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/memcpy_bwamem.cpp -o src/memcpy_bwamem.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/kthread.cpp -o src/kthread.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/kstring.cpp -o src/kstring.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/ksw.cpp -o src/ksw.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/bntseq.cpp -o src/bntseq.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.cpp -o src/bwamem.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/profiling.cpp -o src/profiling.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/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' 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] 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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ 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; } | ^ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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 src/utils.cpp: In function 'int ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)': src/kseq.h:135:109: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 135 | memcpy_bwamem(str->s + str->l, str->m - str->l, ks->buf + ks->begin, i - ks->begin, __FILE__, __LINE__); \ | ^~~~~~~~ src/kseq.h:159:9: note: in expansion of macro '__KS_GETUNTIL' 159 | __KS_GETUNTIL(__read, __bufsize) | ^~~~~~~~~~~~~ src/kseq.h:237:9: note: in expansion of macro 'KSTREAM_INIT' 237 | KSTREAM_INIT(type_t, __read, 16384) \ | ^~~~~~~~~~~~ src/utils.cpp:50:1: note: in expansion of macro 'KSEQ_INIT2' 50 | KSEQ_INIT2(, gzFile, err_gzread) | ^~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/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 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", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~~~~ | | | int64_t {aka long long int} src/bandedSWA.cpp:106:34: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~~~~ | | | int64_t {aka long long int} src/bandedSWA.cpp:106:39: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~ | | | int64_t {aka long long int} src/bandedSWA.cpp:106:44: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~~~~ | | | int64_t {aka long long int} 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", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, 108 | totalTicks); | ~~~~~~~~~~ | | | int64_t {aka long long int} 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/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 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/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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/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*)': 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); | ~~^ ~~~~~~~~~~~ | | | | | 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] 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; } | ^ 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: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; } | ^ 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: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; } | ^ 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: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; } | ^ src/ksort.h:253:25: note: in expansion of macro 'KSORT_SWAP' 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ 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; } | ^ src/ksort.h:259:33: note: in expansion of macro 'KSORT_SWAP' 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ 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; } | ^ src/ksort.h:261:25: note: in expansion of macro 'KSORT_SWAP' 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro 'KSORT_INIT' 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ 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; } | ^ 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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ 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; } | ^ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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: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; } | ^ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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: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; } | ^ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/bwamem.cpp: In function 'mem_alnreg_t ks_ksmall_mem_ars_hash2(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; } | ^ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/bwamem.cpp: In function 'int test_and_merge(const mem_opt_t*, int64_t, mem_chain_t*, const mem_seed_t*, int, int)': 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/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:686:25: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 686 | fprintf(stderr, "[%0.4d] REA Re-allocating min_intv, query_pos, & rid\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:723:29: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 723 | fprintf(stderr, "[%0.4d] REA Re-allocating2 SMEM data structures due to enc_qdb\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:730:50: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long long int} | %lld src/bwamem.cpp:730:57: warning: format '%d' expects argument of type 'int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long long int} | %lld src/bwamem.cpp:765:59: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 765 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long long int} | %lld src/bwamem.cpp:765:66: warning: format '%d' expects argument of type 'int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 765 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long 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", | ~~^ | | | long int | %lld 913 | s.rbeg, s.len, cnt-1, p->n, p->m, num_smem); | ~~~~~~ | | | int64_t {aka long long int} src/bwamem.cpp:912:94: warning: format '%ld' expects argument of type 'long int', but argument 8 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", | ~~^ | | | long int | %lld 913 | s.rbeg, s.len, cnt-1, p->n, p->m, num_smem); | ~~~~~~~~ | | | 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:1048:51: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 1048 | fprintf(stderr, "Error [bug]: num_smem: %ld are more than allocated space %ld.\n", | ~~^ | | | long int | %lld 1049 | num_smem, *wsize_mem); | ~~~~~~~~ | | | int64_t {aka long long int} src/bwamem.cpp:1048:85: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 1048 | fprintf(stderr, "Error [bug]: num_smem: %ld are more than allocated space %ld.\n", | ~~^ | | | long int | %lld 1049 | num_smem, *wsize_mem); | ~~~~~~~~~~ | | | int64_t {aka long long int} In file included from src/bwa.h:38, from src/bwamem.h:36: src/bwamem.cpp:1052:18: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 1052 | printf_(VER, "6. Done! mem_collect_smem, num_smem: %ld\n", num_smem); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~ | | | int64_t {aka long long int} src/macro.h:39:41: note: in definition of macro 'printf_' 39 | fprintf(stderr, y); \ | ^ src/bwamem.cpp:1052:58: note: format string is defined here 1052 | printf_(VER, "6. Done! mem_collect_smem, num_smem: %ld\n", num_smem); | ~~^ | | | 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/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/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/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2260:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2260 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2280:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2280 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2333:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2333 | fprintf(stderr, "[0000] [%0.4d] Re-allocating seqPairArrays Right\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2358:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2358 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -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 -Wl,-z,relro -Wl,-z,now src/main.o libbwa.a -lpthread -lm -lz -L. -lbwa -Lext/safestringlib -lsafestring -o bwa-mem2.sse41 make[3]: Leaving 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' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' make arch=sse42 EXE=bwa-mem2.sse42 CXX=g++ all make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1' 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/fastmap.cpp -o src/fastmap.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/bwtindex.cpp -o src/bwtindex.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/utils.cpp -o src/utils.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/memcpy_bwamem.cpp -o src/memcpy_bwamem.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/kthread.cpp -o src/kthread.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/kstring.cpp -o src/kstring.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/ksw.cpp -o src/ksw.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/bntseq.cpp -o src/bntseq.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.cpp -o src/bwamem.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/profiling.cpp -o src/profiling.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/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] 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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ 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; } | ^ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/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 src/utils.cpp: In function 'int ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)': src/kseq.h:135:109: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 135 | memcpy_bwamem(str->s + str->l, str->m - str->l, ks->buf + ks->begin, i - ks->begin, __FILE__, __LINE__); \ | ^~~~~~~~ src/kseq.h:159:9: note: in expansion of macro '__KS_GETUNTIL' 159 | __KS_GETUNTIL(__read, __bufsize) | ^~~~~~~~~~~~~ src/kseq.h:237:9: note: in expansion of macro 'KSTREAM_INIT' 237 | KSTREAM_INIT(type_t, __read, 16384) \ | ^~~~~~~~~~~~ src/utils.cpp:50:1: note: in expansion of macro 'KSEQ_INIT2' 50 | KSEQ_INIT2(, gzFile, err_gzread) | ^~~~~~~~~~ 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 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 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", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~~~~ | | | int64_t {aka long long int} src/bandedSWA.cpp:106:34: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~~~~ | | | int64_t {aka long long int} src/bandedSWA.cpp:106:39: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~ | | | int64_t {aka long long int} src/bandedSWA.cpp:106:44: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~~~~ | | | int64_t {aka long long int} 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", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, 108 | totalTicks); | ~~~~~~~~~~ | | | 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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 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/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: 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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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); | ~~^ ~~~~~~~~~~ | | | | 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 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__); | ^~~~~~~~ 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.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", | ~~^ | | | 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; } | ^ 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: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; } | ^ 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: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; } | ^ 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: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; } | ^ src/ksort.h:253:25: note: in expansion of macro 'KSORT_SWAP' 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ 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; } | ^ src/ksort.h:259:33: note: in expansion of macro 'KSORT_SWAP' 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ 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; } | ^ src/ksort.h:261:25: note: in expansion of macro 'KSORT_SWAP' 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro 'KSORT_INIT' 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ 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; } | ^ 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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ 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; } | ^ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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; } | ^ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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; } | ^ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/bwamem.cpp: In function 'mem_alnreg_t ks_ksmall_mem_ars_hash2(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; } | ^ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/bwamem.cpp: In function 'int test_and_merge(const mem_opt_t*, int64_t, mem_chain_t*, const mem_seed_t*, int, int)': 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/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:686:25: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 686 | fprintf(stderr, "[%0.4d] REA Re-allocating min_intv, query_pos, & rid\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:723:29: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 723 | fprintf(stderr, "[%0.4d] REA Re-allocating2 SMEM data structures due to enc_qdb\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:730:50: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long long int} | %lld src/bwamem.cpp:730:57: warning: format '%d' expects argument of type 'int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long long int} | %lld src/bwamem.cpp:765:59: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 765 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long long int} | %lld src/bwamem.cpp:765:66: warning: format '%d' expects argument of type 'int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 765 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long 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", | ~~^ | | | long int | %lld 913 | s.rbeg, s.len, cnt-1, p->n, p->m, num_smem); | ~~~~~~ | | | int64_t {aka long long int} src/bwamem.cpp:912:94: warning: format '%ld' expects argument of type 'long int', but argument 8 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", | ~~^ | | | long int | %lld 913 | s.rbeg, s.len, cnt-1, p->n, p->m, num_smem); | ~~~~~~~~ | | | 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:1048:51: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 1048 | fprintf(stderr, "Error [bug]: num_smem: %ld are more than allocated space %ld.\n", | ~~^ | | | long int | %lld 1049 | num_smem, *wsize_mem); | ~~~~~~~~ | | | int64_t {aka long long int} src/bwamem.cpp:1048:85: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 1048 | fprintf(stderr, "Error [bug]: num_smem: %ld are more than allocated space %ld.\n", | ~~^ | | | long int | %lld 1049 | num_smem, *wsize_mem); | ~~~~~~~~~~ | | | int64_t {aka long long int} In file included from src/bwa.h:38, from src/bwamem.h:36: src/bwamem.cpp:1052:18: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 1052 | printf_(VER, "6. Done! mem_collect_smem, num_smem: %ld\n", num_smem); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~ | | | int64_t {aka long long int} src/macro.h:39:41: note: in definition of macro 'printf_' 39 | fprintf(stderr, y); \ | ^ src/bwamem.cpp:1052:58: note: format string is defined here 1052 | printf_(VER, "6. Done! mem_collect_smem, num_smem: %ld\n", num_smem); | ~~^ | | | 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/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/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/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2260:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2260 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2280:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2280 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2333:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2333 | fprintf(stderr, "[0000] [%0.4d] Re-allocating seqPairArrays Right\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2358:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2358 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -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 -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' 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' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' make arch=avx EXE=bwa-mem2.avx CXX=g++ all make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1' 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/fastmap.cpp -o src/fastmap.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 -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/bwtindex.cpp -o src/bwtindex.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 -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/utils.cpp -o src/utils.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 -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/memcpy_bwamem.cpp -o src/memcpy_bwamem.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 -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/kthread.cpp -o src/kthread.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 -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/kstring.cpp -o src/kstring.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 -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/ksw.cpp -o src/ksw.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 -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/bntseq.cpp -o src/bntseq.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 -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/bwamem.cpp -o src/bwamem.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 -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/profiling.cpp -o src/profiling.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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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' 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] 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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ 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; } | ^ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/utils.cpp: In function 'int ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)': src/kseq.h:135:109: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 135 | memcpy_bwamem(str->s + str->l, str->m - str->l, ks->buf + ks->begin, i - ks->begin, __FILE__, __LINE__); \ | ^~~~~~~~ src/kseq.h:159:9: note: in expansion of macro '__KS_GETUNTIL' 159 | __KS_GETUNTIL(__read, __bufsize) | ^~~~~~~~~~~~~ src/kseq.h:237:9: note: in expansion of macro 'KSTREAM_INIT' 237 | KSTREAM_INIT(type_t, __read, 16384) \ | ^~~~~~~~~~~~ src/utils.cpp:50:1: note: in expansion of macro 'KSEQ_INIT2' 50 | KSEQ_INIT2(, gzFile, err_gzread) | ^~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/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/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 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/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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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/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", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~~~~ | | | int64_t {aka long long int} src/bandedSWA.cpp:106:34: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~~~~ | | | int64_t {aka long long int} src/bandedSWA.cpp:106:39: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~ | | | int64_t {aka long long int} src/bandedSWA.cpp:106:44: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~~~~ | | | int64_t {aka long long int} 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", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, 108 | totalTicks); | ~~~~~~~~~~ | | | 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); | ~~^ ~~~~~~~~~~~ | | | | | 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] 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; } | ^ 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: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; } | ^ 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: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; } | ^ 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: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; } | ^ src/ksort.h:253:25: note: in expansion of macro 'KSORT_SWAP' 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ 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; } | ^ src/ksort.h:259:33: note: in expansion of macro 'KSORT_SWAP' 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ 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; } | ^ src/ksort.h:261:25: note: in expansion of macro 'KSORT_SWAP' 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro 'KSORT_INIT' 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ 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; } | ^ 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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ 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; } | ^ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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; } | ^ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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; } | ^ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/bwamem.cpp: In function 'mem_alnreg_t ks_ksmall_mem_ars_hash2(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; } | ^ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/bwamem.cpp: In function 'int test_and_merge(const mem_opt_t*, int64_t, mem_chain_t*, const mem_seed_t*, int, int)': 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/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:686:25: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 686 | fprintf(stderr, "[%0.4d] REA Re-allocating min_intv, query_pos, & rid\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:723:29: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 723 | fprintf(stderr, "[%0.4d] REA Re-allocating2 SMEM data structures due to enc_qdb\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:730:50: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long long int} | %lld src/bwamem.cpp:730:57: warning: format '%d' expects argument of type 'int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long long int} | %lld src/bwamem.cpp:765:59: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 765 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long long int} | %lld src/bwamem.cpp:765:66: warning: format '%d' expects argument of type 'int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 765 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long 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", | ~~^ | | | long int | %lld 913 | s.rbeg, s.len, cnt-1, p->n, p->m, num_smem); | ~~~~~~ | | | int64_t {aka long long int} src/bwamem.cpp:912:94: warning: format '%ld' expects argument of type 'long int', but argument 8 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", | ~~^ | | | long int | %lld 913 | s.rbeg, s.len, cnt-1, p->n, p->m, num_smem); | ~~~~~~~~ | | | 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:1048:51: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 1048 | fprintf(stderr, "Error [bug]: num_smem: %ld are more than allocated space %ld.\n", | ~~^ | | | long int | %lld 1049 | num_smem, *wsize_mem); | ~~~~~~~~ | | | int64_t {aka long long int} src/bwamem.cpp:1048:85: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 1048 | fprintf(stderr, "Error [bug]: num_smem: %ld are more than allocated space %ld.\n", | ~~^ | | | long int | %lld 1049 | num_smem, *wsize_mem); | ~~~~~~~~~~ | | | int64_t {aka long long int} In file included from src/bwa.h:38, from src/bwamem.h:36: src/bwamem.cpp:1052:18: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 1052 | printf_(VER, "6. Done! mem_collect_smem, num_smem: %ld\n", num_smem); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~ | | | int64_t {aka long long int} src/macro.h:39:41: note: in definition of macro 'printf_' 39 | fprintf(stderr, y); \ | ^ src/bwamem.cpp:1052:58: note: format string is defined here 1052 | printf_(VER, "6. Done! mem_collect_smem, num_smem: %ld\n", num_smem); | ~~^ | | | 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/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/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/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2260:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2260 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2280:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2280 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2333:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2333 | fprintf(stderr, "[0000] [%0.4d] Re-allocating seqPairArrays Right\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2358:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2358 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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' 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' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' make arch=avx2 EXE=bwa-mem2.avx2 CXX=g++ all make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1' 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/fastmap.cpp -o src/fastmap.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/bwtindex.cpp -o src/bwtindex.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/utils.cpp -o src/utils.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/memcpy_bwamem.cpp -o src/memcpy_bwamem.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/kthread.cpp -o src/kthread.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/kstring.cpp -o src/kstring.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/ksw.cpp -o src/ksw.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/bntseq.cpp -o src/bntseq.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.cpp -o src/bwamem.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/profiling.cpp -o src/profiling.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/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 -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 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 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/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 -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/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 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] 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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ 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; } | ^ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/utils.cpp: In function 'int ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)': src/kseq.h:135:109: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 135 | memcpy_bwamem(str->s + str->l, str->m - str->l, ks->buf + ks->begin, i - ks->begin, __FILE__, __LINE__); \ | ^~~~~~~~ src/kseq.h:159:9: note: in expansion of macro '__KS_GETUNTIL' 159 | __KS_GETUNTIL(__read, __bufsize) | ^~~~~~~~~~~~~ src/kseq.h:237:9: note: in expansion of macro 'KSTREAM_INIT' 237 | KSTREAM_INIT(type_t, __read, 16384) \ | ^~~~~~~~~~~~ src/utils.cpp:50:1: note: in expansion of macro 'KSEQ_INIT2' 50 | KSEQ_INIT2(, gzFile, err_gzread) | ^~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/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/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 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/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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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_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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 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", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~~~~ | | | int64_t {aka long long int} src/bandedSWA.cpp:106:34: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~~~~ | | | int64_t {aka long long int} src/bandedSWA.cpp:106:39: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~ | | | int64_t {aka long long int} src/bandedSWA.cpp:106:44: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~~~~ | | | int64_t {aka long long int} 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", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, 108 | totalTicks); | ~~~~~~~~~~ | | | 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: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ In file included from src/main.h:36, from src/main.cpp:35: src/kstring.h: In function 'int kputsn(const char*, int, kstring_t*)': src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ 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__); | ^~~~~~~~ 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); | ~~^ ~~~~~~~~~~~ | | | | | 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); | ~~^ ~~~~~~~~~~ | | | | 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/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; } | ^ 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: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; } | ^ 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: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; } | ^ 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: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; } | ^ src/ksort.h:253:25: note: in expansion of macro 'KSORT_SWAP' 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ 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; } | ^ src/ksort.h:259:33: note: in expansion of macro 'KSORT_SWAP' 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ 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; } | ^ src/ksort.h:261:25: note: in expansion of macro 'KSORT_SWAP' 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro 'KSORT_INIT' 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ 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; } | ^ 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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ 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; } | ^ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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; } | ^ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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; } | ^ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/bwamem.cpp: In function 'mem_alnreg_t ks_ksmall_mem_ars_hash2(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; } | ^ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/bwamem.cpp: In function 'int test_and_merge(const mem_opt_t*, int64_t, mem_chain_t*, const mem_seed_t*, int, int)': 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/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:686:25: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 686 | fprintf(stderr, "[%0.4d] REA Re-allocating min_intv, query_pos, & rid\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:723:29: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 723 | fprintf(stderr, "[%0.4d] REA Re-allocating2 SMEM data structures due to enc_qdb\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:730:50: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long long int} | %lld src/bwamem.cpp:730:57: warning: format '%d' expects argument of type 'int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long long int} | %lld src/bwamem.cpp:765:59: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 765 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long long int} | %lld src/bwamem.cpp:765:66: warning: format '%d' expects argument of type 'int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 765 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long 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", | ~~^ | | | long int | %lld 913 | s.rbeg, s.len, cnt-1, p->n, p->m, num_smem); | ~~~~~~ | | | int64_t {aka long long int} src/bwamem.cpp:912:94: warning: format '%ld' expects argument of type 'long int', but argument 8 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", | ~~^ | | | long int | %lld 913 | s.rbeg, s.len, cnt-1, p->n, p->m, num_smem); | ~~~~~~~~ | | | 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:1048:51: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 1048 | fprintf(stderr, "Error [bug]: num_smem: %ld are more than allocated space %ld.\n", | ~~^ | | | long int | %lld 1049 | num_smem, *wsize_mem); | ~~~~~~~~ | | | int64_t {aka long long int} src/bwamem.cpp:1048:85: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 1048 | fprintf(stderr, "Error [bug]: num_smem: %ld are more than allocated space %ld.\n", | ~~^ | | | long int | %lld 1049 | num_smem, *wsize_mem); | ~~~~~~~~~~ | | | int64_t {aka long long int} In file included from src/bwa.h:38, from src/bwamem.h:36: src/bwamem.cpp:1052:18: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 1052 | printf_(VER, "6. Done! mem_collect_smem, num_smem: %ld\n", num_smem); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~ | | | int64_t {aka long long int} src/macro.h:39:41: note: in definition of macro 'printf_' 39 | fprintf(stderr, y); \ | ^ src/bwamem.cpp:1052:58: note: format string is defined here 1052 | printf_(VER, "6. Done! mem_collect_smem, num_smem: %ld\n", num_smem); | ~~^ | | | 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/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/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/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2260:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2260 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2280:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2280 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2333:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2333 | fprintf(stderr, "[0000] [%0.4d] Re-allocating seqPairArrays Right\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2358:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2358 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now src/main.o libbwa.a -lpthread -lm -lz -L. -lbwa -Lext/safestringlib -lsafestring -o bwa-mem2.avx2 make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1' 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' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' make arch=avx512 EXE=bwa-mem2.avx512bw CXX=g++ all make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1' 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 -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 -Isrc -Iext/safestringlib/include src/fastmap.cpp -o src/fastmap.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 -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 -Isrc -Iext/safestringlib/include src/bwtindex.cpp -o src/bwtindex.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 -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 -Isrc -Iext/safestringlib/include src/utils.cpp -o src/utils.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 -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 -Isrc -Iext/safestringlib/include src/memcpy_bwamem.cpp -o src/memcpy_bwamem.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 -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 -Isrc -Iext/safestringlib/include src/kthread.cpp -o src/kthread.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 -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 -Isrc -Iext/safestringlib/include src/kstring.cpp -o src/kstring.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 -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 -Isrc -Iext/safestringlib/include src/ksw.cpp -o src/ksw.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 -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 -Isrc -Iext/safestringlib/include src/bntseq.cpp -o src/bntseq.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 -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 -Isrc -Iext/safestringlib/include src/bwamem.cpp -o src/bwamem.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 -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 -Isrc -Iext/safestringlib/include src/profiling.cpp -o src/profiling.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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 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 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] 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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_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/utils.cpp:46:1: note: in expansion of macro 'KSORT_INIT' 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ 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; } | ^ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/utils.cpp:47:1: note: in expansion of macro 'KSORT_INIT' 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ 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/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 src/utils.cpp: In function 'int ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)': src/kseq.h:135:109: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 135 | memcpy_bwamem(str->s + str->l, str->m - str->l, ks->buf + ks->begin, i - ks->begin, __FILE__, __LINE__); \ | ^~~~~~~~ src/kseq.h:159:9: note: in expansion of macro '__KS_GETUNTIL' 159 | __KS_GETUNTIL(__read, __bufsize) | ^~~~~~~~~~~~~ src/kseq.h:237:9: note: in expansion of macro 'KSTREAM_INIT' 237 | KSTREAM_INIT(type_t, __read, 16384) \ | ^~~~~~~~~~~~ src/utils.cpp:50:1: note: in expansion of macro 'KSEQ_INIT2' 50 | KSEQ_INIT2(, gzFile, err_gzread) | ^~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 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/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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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 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", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~~~~ | | | int64_t {aka long long int} src/bandedSWA.cpp:106:34: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~~~~ | | | int64_t {aka long long int} src/bandedSWA.cpp:106:39: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~ | | | int64_t {aka long long int} src/bandedSWA.cpp:106:44: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int64_t' {aka 'long long int'} [-Wformat=] 106 | printf("cost breakup: %ld, %ld, %ld, %ld, %ld\n", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, | ~~~~~~~~~~ | | | int64_t {aka long long int} 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", | ~~^ | | | long int | %lld 107 | sort1Ticks, setupTicks, swTicks, sort2Ticks, 108 | totalTicks); | ~~~~~~~~~~ | | | 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] 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__); | ^~~~~~~~ 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: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; } | ^ 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: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; } | ^ 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: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; } | ^ 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: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; } | ^ src/ksort.h:253:25: note: in expansion of macro 'KSORT_SWAP' 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ 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; } | ^ src/ksort.h:259:33: note: in expansion of macro 'KSORT_SWAP' 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ 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; } | ^ src/ksort.h:261:25: note: in expansion of macro 'KSORT_SWAP' 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro 'KSORT_INIT' 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ 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; } | ^ 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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_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:65:1: note: in expansion of macro 'KSORT_INIT' 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ 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; } | ^ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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:153:1: note: in expansion of macro 'KSORT_INIT' 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ 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; } | ^ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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:156:1: note: in expansion of macro 'KSORT_INIT' 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ 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; } | ^ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ 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:159:1: note: in expansion of macro 'KSORT_INIT' 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/bwamem.cpp: In function 'mem_alnreg_t ks_ksmall_mem_ars_hash2(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; } | ^ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ 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:162:1: note: in expansion of macro 'KSORT_INIT' 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/bwamem.cpp: In function 'int test_and_merge(const mem_opt_t*, int64_t, mem_chain_t*, const mem_seed_t*, int, int)': 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/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:686:25: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 686 | fprintf(stderr, "[%0.4d] REA Re-allocating min_intv, query_pos, & rid\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:723:29: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 723 | fprintf(stderr, "[%0.4d] REA Re-allocating2 SMEM data structures due to enc_qdb\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:730:50: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long long int} | %lld src/bwamem.cpp:730:57: warning: format '%d' expects argument of type 'int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long long int} | %lld src/bwamem.cpp:765:59: warning: format '%d' expects argument of type 'int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 765 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long long int} | %lld src/bwamem.cpp:765:66: warning: format '%d' expects argument of type 'int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 765 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long 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", | ~~^ | | | long int | %lld 913 | s.rbeg, s.len, cnt-1, p->n, p->m, num_smem); | ~~~~~~ | | | int64_t {aka long long int} src/bwamem.cpp:912:94: warning: format '%ld' expects argument of type 'long int', but argument 8 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", | ~~^ | | | long int | %lld 913 | s.rbeg, s.len, cnt-1, p->n, p->m, num_smem); | ~~~~~~~~ | | | 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:1048:51: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 1048 | fprintf(stderr, "Error [bug]: num_smem: %ld are more than allocated space %ld.\n", | ~~^ | | | long int | %lld 1049 | num_smem, *wsize_mem); | ~~~~~~~~ | | | int64_t {aka long long int} src/bwamem.cpp:1048:85: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int64_t' {aka 'long long int'} [-Wformat=] 1048 | fprintf(stderr, "Error [bug]: num_smem: %ld are more than allocated space %ld.\n", | ~~^ | | | long int | %lld 1049 | num_smem, *wsize_mem); | ~~~~~~~~~~ | | | int64_t {aka long long int} In file included from src/bwa.h:38, from src/bwamem.h:36: src/bwamem.cpp:1052:18: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t' {aka 'long long int'} [-Wformat=] 1052 | printf_(VER, "6. Done! mem_collect_smem, num_smem: %ld\n", num_smem); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~ | | | int64_t {aka long long int} src/macro.h:39:41: note: in definition of macro 'printf_' 39 | fprintf(stderr, y); \ | ^ src/bwamem.cpp:1052:58: note: format string is defined here 1052 | printf_(VER, "6. Done! mem_collect_smem, num_smem: %ld\n", num_smem); | ~~^ | | | 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/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/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/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2260:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2260 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2280:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2280 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2333:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2333 | fprintf(stderr, "[0000] [%0.4d] Re-allocating seqPairArrays Right\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2358:41: warning: '0' flag ignored with precision and '%d' gnu_printf format [-Wformat=] 2358 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 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' 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 -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' help2man --no-discard-stderr --version-string="2.2.1" \ --help-option=' ' --no-info ./bwa-mem2 --name="Sequence alignment using Burrows-Wheeler Transform" \ > debian/bwa-mem2.1 help2man --no-discard-stderr --version-string="2.2.1" \ --help-option=' ' --no-info './bwa-mem2 mem' \ --include <(echo -e "[NAME]\nbwa-mem2_mem \- Sequence alignment using Burrows-Wheeler Transform") \ > debian/bwa-mem2-mem.1 make[1]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/bwa-mem2/ dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb 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-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) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration 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