Diff of the two buildlogs:
--
--- b1/build.log 2021-07-05 03:01:15.456523475 +0000
+++ b2/build.log 2021-07-05 03:05:38.526658138 +0000
@@ -1,8 +1,6 @@
-unshare: unshare failed: Cannot allocate memory
-W: pbuilder: unshare CLONE_NEWNET not available
-I: pbuilder: network access is available during build!
-I: Current time: Sun Jul 4 14:49:38 -12 2021
-I: pbuilder-time-stamp: 1625453378
+I: pbuilder: network access will be disabled during build
+I: Current time: Sun Aug 7 23:24:15 +14 2022
+I: pbuilder-time-stamp: 1659864255
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz]
I: copying local configuration
@@ -19,8 +17,8 @@
I: copying [./fasta3_36.3.8h.2020-02-11-3.debian.tar.xz]
I: Extracting source
gpgv: unknown type of key resource 'trustedkeys.kbx'
-gpgv: keyblock resource '/tmp/dpkg-verify-sig.byvYDo__/trustedkeys.kbx': General error
-gpgv: Signature made Fri Apr 17 21:54:39 2020 -12
+gpgv: keyblock resource '/tmp/dpkg-verify-sig.Sul6rHQf/trustedkeys.kbx': General error
+gpgv: Signature made Sat Apr 18 23:54:39 2020 +14
gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./fasta3_36.3.8h.2020-02-11-3.dsc
@@ -34,137 +32,171 @@
dpkg-source: info: applying adjust-scripts
I: Not using root during the build.
I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/15799/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/26194/tmp/hooks/D01_modify_environment starting
+debug: Running on ionos16-i386.
+I: Changing host+domainname to test build reproducibility
+I: Adding a custom variable just for the fun of it...
+I: Changing /bin/sh to bash
+Removing 'diversion of /bin/sh to /bin/sh.distrib by dash'
+Adding 'diversion of /bin/sh to /bin/sh.distrib by bash'
+Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash'
+Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash'
+I: Setting pbuilder2's login shell to /bin/bash
+I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
+I: user script /srv/workspace/pbuilder/26194/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/26194/tmp/hooks/D02_print_environment starting
I: set
- BUILDDIR='/build'
- 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,-fixfilepath parallel=10'
- DISTRIBUTION=''
- HOME='/root'
- HOST_ARCH='i386'
+ BASH=/bin/sh
+ BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath
+ BASH_ALIASES=()
+ BASH_ARGC=()
+ BASH_ARGV=()
+ BASH_CMDS=()
+ BASH_LINENO=([0]="12" [1]="0")
+ BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
+ BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="i686-pc-linux-gnu")
+ BASH_VERSION='5.1.4(1)-release'
+ BUILDDIR=/build
+ BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
+ BUILDUSERNAME=pbuilder2
+ BUILD_ARCH=i386
+ DEBIAN_FRONTEND=noninteractive
+ DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=18'
+ DIRSTACK=()
+ DISTRIBUTION=
+ EUID=0
+ FUNCNAME=([0]="Echo" [1]="main")
+ GROUPS=()
+ HOME=/root
+ HOSTNAME=i-capture-the-hostname
+ HOSTTYPE=i686
+ HOST_ARCH=i386
IFS='
'
- INVOCATION_ID='cc6150ae80084bf98738bf52f7408d18'
- 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='15799'
- PS1='# '
- PS2='> '
+ INVOCATION_ID=b0a5b9eaa16c41c8b129616464f27124
+ LANG=C
+ LANGUAGE=de_CH:de
+ LC_ALL=C
+ LD_LIBRARY_PATH=/usr/lib/libeatmydata
+ LD_PRELOAD=libeatmydata.so
+ MACHTYPE=i686-pc-linux-gnu
+ MAIL=/var/mail/root
+ OPTERR=1
+ OPTIND=1
+ OSTYPE=linux-gnu
+ PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
+ PBCURRENTCOMMANDLINEOPERATION=build
+ PBUILDER_OPERATION=build
+ PBUILDER_PKGDATADIR=/usr/share/pbuilder
+ PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
+ PBUILDER_SYSCONFDIR=/etc
+ PIPESTATUS=([0]="0")
+ POSIXLY_CORRECT=y
+ PPID=26194
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/tmp.RsLRQnrC9I/pbuilderrc_th7p --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.RsLRQnrC9I/b1 --logfile b1/build.log fasta3_36.3.8h.2020-02-11-3.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://78.137.99.97:3128'
+ PWD=/
+ SHELL=/bin/bash
+ SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
+ SHLVL=3
+ SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.RsLRQnrC9I/pbuilderrc_wxIN --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.RsLRQnrC9I/b2 --logfile b2/build.log --extrapackages usrmerge fasta3_36.3.8h.2020-02-11-3.dsc'
+ SUDO_GID=112
+ SUDO_UID=107
+ SUDO_USER=jenkins
+ TERM=unknown
+ TZ=/usr/share/zoneinfo/Etc/GMT-14
+ UID=0
+ USER=root
+ _='I: set'
+ http_proxy=http://85.184.249.68:3128
I: uname -a
- Linux ionos2-i386 4.19.0-17-686-pae #1 SMP Debian 4.19.194-2 (2021-06-21) i686 GNU/Linux
+ Linux i-capture-the-hostname 4.19.0-17-amd64 #1 SMP Debian 4.19.194-2 (2021-06-21) x86_64 GNU/Linux
I: ls -l /bin
- total 5780
- -rwxr-xr-x 1 root root 1367848 Jun 21 14:25 bash
- -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2
- -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat
- lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff
- -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff
- lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep
- -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe
- lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep
- -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep
- -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2
- -rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover
- lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore
- -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore
- -rwxr-xr-x 1 root root 38824 Sep 22 2020 cat
- -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp
- -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod
- -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown
- -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp
- -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash
- -rwxr-xr-x 1 root root 124904 Sep 22 2020 date
- -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd
- -rwxr-xr-x 1 root root 100752 Sep 22 2020 df
- -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir
- -rwxr-xr-x 1 root root 83644 Feb 7 02:38 dmesg
- lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname
- lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname
- -rwxr-xr-x 1 root root 34664 Sep 22 2020 echo
- -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep
- -rwxr-xr-x 1 root root 34664 Sep 22 2020 false
- -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep
- -rwxr-xr-x 1 root root 71928 Feb 7 02:38 findmnt
- -rwsr-xr-x 1 root root 30112 Feb 26 04:12 fusermount
- -rwxr-xr-x 1 root root 210488 Nov 9 2020 grep
- -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip
- -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe
- -rwxr-xr-x 1 root root 100952 Mar 2 11:30 gzip
- -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname
- -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln
- -rwxr-xr-x 1 root root 55572 Feb 7 2020 login
- -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls
- -rwxr-xr-x 1 root root 153124 Feb 7 02:38 lsblk
- -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir
- -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod
- -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp
- -rwxr-xr-x 1 root root 58920 Feb 7 02:38 more
- -rwsr-xr-x 1 root root 50720 Feb 7 02:38 mount
- -rwxr-xr-x 1 root root 13856 Feb 7 02:38 mountpoint
- -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv
- lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname
- lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5
- -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd
- lrwxrwxrwx 1 root root 4 Jun 21 14:25 rbash -> bash
- -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink
- -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm
- -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir
- -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts
- -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed
- lrwxrwxrwx 1 root root 4 Jul 4 02:20 sh -> dash
- -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep
- -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty
- -rwsr-xr-x 1 root root 79396 Feb 7 02:38 su
- -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync
- -rwxr-xr-x 1 root root 602584 Feb 16 21:55 tar
- -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile
- -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch
- -rwxr-xr-x 1 root root 34664 Sep 22 2020 true
- -rwxr-xr-x 1 root root 17768 Feb 26 04:12 ulockmgr_server
- -rwsr-xr-x 1 root root 30236 Feb 7 02:38 umount
- -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname
- -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress
- -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir
- -rwxr-xr-x 1 root root 63024 Feb 7 02:38 wdctl
- lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname
- -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat
- -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp
- -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff
- -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep
- -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep
- -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce
- -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep
- -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless
- -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore
- -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew
-I: user script /srv/workspace/pbuilder/15799/tmp/hooks/D02_print_environment finished
+ total 5776
+ -rwxr-xr-x 1 root root 1367848 Jun 22 2021 bash
+ -rwxr-xr-x 3 root root 38280 Jul 21 2020 bunzip2
+ -rwxr-xr-x 3 root root 38280 Jul 21 2020 bzcat
+ lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff
+ -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff
+ lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep
+ -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe
+ lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep
+ -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep
+ -rwxr-xr-x 3 root root 38280 Jul 21 2020 bzip2
+ -rwxr-xr-x 1 root root 17768 Jul 21 2020 bzip2recover
+ lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore
+ -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore
+ -rwxr-xr-x 1 root root 38824 Sep 23 2020 cat
+ -rwxr-xr-x 1 root root 71624 Sep 23 2020 chgrp
+ -rwxr-xr-x 1 root root 67528 Sep 23 2020 chmod
+ -rwxr-xr-x 1 root root 75752 Sep 23 2020 chown
+ -rwxr-xr-x 1 root root 157960 Sep 23 2020 cp
+ -rwxr-xr-x 1 root root 128724 Dec 11 2020 dash
+ -rwxr-xr-x 1 root root 124904 Sep 23 2020 date
+ -rwxr-xr-x 1 root root 92172 Sep 23 2020 dd
+ -rwxr-xr-x 1 root root 100752 Sep 23 2020 df
+ -rwxr-xr-x 1 root root 153964 Sep 23 2020 dir
+ -rwxr-xr-x 1 root root 83644 Feb 8 2021 dmesg
+ lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname
+ lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname
+ -rwxr-xr-x 1 root root 34664 Sep 23 2020 echo
+ -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep
+ -rwxr-xr-x 1 root root 34664 Sep 23 2020 false
+ -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep
+ -rwxr-xr-x 1 root root 71928 Feb 8 2021 findmnt
+ -rwsr-xr-x 1 root root 30112 Feb 27 2021 fusermount
+ -rwxr-xr-x 1 root root 210488 Nov 10 2020 grep
+ -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip
+ -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe
+ -rwxr-xr-x 1 root root 100952 Mar 3 2021 gzip
+ -rwxr-xr-x 1 root root 21916 Nov 8 2019 hostname
+ -rwxr-xr-x 1 root root 83980 Sep 23 2020 ln
+ -rwxr-xr-x 1 root root 55572 Feb 8 2020 login
+ -rwxr-xr-x 1 root root 153964 Sep 23 2020 ls
+ -rwxr-xr-x 1 root root 153124 Feb 8 2021 lsblk
+ -rwxr-xr-x 1 root root 96328 Sep 23 2020 mkdir
+ -rwxr-xr-x 1 root root 79912 Sep 23 2020 mknod
+ -rwxr-xr-x 1 root root 47048 Sep 23 2020 mktemp
+ -rwxr-xr-x 1 root root 58920 Feb 8 2021 more
+ -rwsr-xr-x 1 root root 50720 Feb 8 2021 mount
+ -rwxr-xr-x 1 root root 13856 Feb 8 2021 mountpoint
+ -rwxr-xr-x 1 root root 157996 Sep 23 2020 mv
+ lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname
+ lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5
+ -rwxr-xr-x 1 root root 38824 Sep 23 2020 pwd
+ lrwxrwxrwx 1 root root 4 Jun 22 2021 rbash -> bash
+ -rwxr-xr-x 1 root root 46984 Sep 23 2020 readlink
+ -rwxr-xr-x 1 root root 75720 Sep 23 2020 rm
+ -rwxr-xr-x 1 root root 46984 Sep 23 2020 rmdir
+ -rwxr-xr-x 1 root root 22292 Sep 28 2020 run-parts
+ -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed
+ lrwxrwxrwx 1 root root 4 Aug 7 23:24 sh -> bash
+ lrwxrwxrwx 1 root root 4 Aug 7 05:46 sh.distrib -> dash
+ -rwxr-xr-x 1 root root 34696 Sep 23 2020 sleep
+ -rwxr-xr-x 1 root root 83880 Sep 23 2020 stty
+ -rwsr-xr-x 1 root root 79396 Feb 8 2021 su
+ -rwxr-xr-x 1 root root 34696 Sep 23 2020 sync
+ -rwxr-xr-x 1 root root 602584 Feb 17 2021 tar
+ -rwxr-xr-x 1 root root 13860 Sep 28 2020 tempfile
+ -rwxr-xr-x 1 root root 108520 Sep 23 2020 touch
+ -rwxr-xr-x 1 root root 34664 Sep 23 2020 true
+ -rwxr-xr-x 1 root root 17768 Feb 27 2021 ulockmgr_server
+ -rwsr-xr-x 1 root root 30236 Feb 8 2021 umount
+ -rwxr-xr-x 1 root root 34664 Sep 23 2020 uname
+ -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress
+ -rwxr-xr-x 1 root root 153964 Sep 23 2020 vdir
+ -rwxr-xr-x 1 root root 63024 Feb 8 2021 wdctl
+ lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname
+ -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat
+ -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp
+ -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff
+ -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep
+ -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep
+ -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce
+ -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep
+ -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless
+ -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore
+ -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew
+I: user script /srv/workspace/pbuilder/26194/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
@@ -234,7 +266,7 @@
Get: 30 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 31 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB]
Get: 32 http://deb.debian.org/debian bullseye/main i386 libsimde-dev all 0.7.2-4 [259 kB]
-Fetched 18.8 MB in 9s (2160 kB/s)
+Fetched 18.8 MB in 0s (77.4 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package bsdextrautils.
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19675 files and directories currently installed.)
@@ -377,8 +409,44 @@
Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following additional packages will be installed:
+ libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl
+The following NEW packages will be installed:
+ libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge
+0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded.
+Need to get 59.5 kB of archives.
+After this operation, 157 kB of additional disk space will be used.
+Get:1 http://deb.debian.org/debian bullseye/main i386 libnumber-compare-perl all 0.03-1.1 [6956 B]
+Get:2 http://deb.debian.org/debian bullseye/main i386 libtext-glob-perl all 0.11-1 [8888 B]
+Get:3 http://deb.debian.org/debian bullseye/main i386 libfile-find-rule-perl all 0.34-1 [30.6 kB]
+Get:4 http://deb.debian.org/debian bullseye/main i386 usrmerge all 25 [13.0 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 59.5 kB in 0s (5787 kB/s)
+Selecting previously unselected package libnumber-compare-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 ... 21797 files and directories currently installed.)
+Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ...
+Unpacking libnumber-compare-perl (0.03-1.1) ...
+Selecting previously unselected package libtext-glob-perl.
+Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ...
+Unpacking libtext-glob-perl (0.11-1) ...
+Selecting previously unselected package libfile-find-rule-perl.
+Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ...
+Unpacking libfile-find-rule-perl (0.34-1) ...
+Selecting previously unselected package usrmerge.
+Preparing to unpack .../archives/usrmerge_25_all.deb ...
+Unpacking usrmerge (25) ...
+Setting up libtext-glob-perl (0.11-1) ...
+Setting up libnumber-compare-perl (0.03-1.1) ...
+Setting up libfile-find-rule-perl (0.34-1) ...
+Setting up usrmerge (25) ...
+The system has been successfully converted.
+Processing triggers for man-db (2.9.4-2) ...
+Not building database; man-db/auto-update is not 'true'.
I: Building the package
-I: Running cd /build/fasta3-36.3.8h.2020-02-11/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b
+I: Running cd /build/fasta3-36.3.8h.2020-02-11/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b
dpkg-buildpackage: info: source package fasta3
dpkg-buildpackage: info: source version 36.3.8h.2020-02-11-3
dpkg-buildpackage: info: source distribution unstable
@@ -404,7 +472,7 @@
debian/rules override_dh_auto_build
make[1]: Entering directory '/build/fasta3-36.3.8h.2020-02-11'
dh_auto_build --sourcedirectory make --builddirectory src --buildsystem makefile -- -f "../make/Makefile.linux64"
- cd src && make -j10 "INSTALL=install --strip-program=true" -f ../make/Makefile.linux64
+ cd src && make -j18 "INSTALL=install --strip-program=true" -f ../make/Makefile.linux64
make[2]: Entering directory '/build/fasta3-36.3.8h.2020-02-11/src'
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DCOMP_THR -DCOMP_MLIB -c comp_lib9.c -o comp_mthr9.o
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c work_thr2.c
@@ -416,6 +484,15 @@
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DCOMP_THR -c mshowalign2.c -o mshowalign2_t.o
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c htime.c
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c apam.c
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c doinit.c
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTA initfa.c -o init_fa.o
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DLOCAL_SCORE -c scaleswn.c -o scale_se.o
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c karlin.c
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c dropnfa.c -o drop_nfa.o
+cc -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o wm_align.o wm_align.c
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DFASTA -c cal_cons2.c -o calcons_fa.o
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c nmgetlib.c -o lgetlib.o
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c mmgetaa.c -o lgetaa_m.o
mshowalign2.c: In function 'showalign':
mshowalign2.c:614:57: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
614 | fprintf(stderr," mshowalign: nc/maxc: %d/%d seqc0/1: %lu/%lu\n",
@@ -437,11 +514,13 @@
| ~~~~~~~~~~~~~
| |
| size_t {aka unsigned int}
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c doinit.c
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTA initfa.c -o init_fa.o
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DLOCAL_SCORE -c scaleswn.c -o scale_se.o
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c karlin.c
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c dropnfa.c -o drop_nfa.o
+dropnfa.c: In function 'init_work':
+dropnfa.c:306:77: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'unsigned int' [-Wformat=]
+ 306 | fprintf (stderr,"*** error [%s:%d] - cannot allocate diagonal arrays: %lu\n",
+ | ~~^
+ | |
+ | long unsigned int
+ | %u
scaleswn.c: In function 'process_hist':
scaleswn.c:255:55: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
255 | fprintf(stderr," cannot allocate pstat_union: %ld\n",sizeof(struct pstat_str));
@@ -450,25 +529,6 @@
| | unsigned int
| long int
| %d
-initfa.c: In function 'alloc_pam2p':
-initfa.c:2001:39: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
- 2001 | "Cannot reallocate pam2p[0]: %ld\n", (nsq+1)*len*sizeof(int));
- | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~
- | | |
- | long int unsigned int
- | %d
-cc -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o wm_align.o wm_align.c
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DFASTA -c cal_cons2.c -o calcons_fa.o
-dropnfa.c: In function 'init_work':
-dropnfa.c:306:77: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'unsigned int' [-Wformat=]
- 306 | fprintf (stderr,"*** error [%s:%d] - cannot allocate diagonal arrays: %lu\n",
- | ~~^
- | |
- | long unsigned int
- | %u
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c nmgetlib.c -o lgetlib.o
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c mmgetaa.c -o lgetaa_m.o
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c c_dispn.c
nmgetlib.c: In function 'open_lib':
nmgetlib.c:403:52: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
403 | fprintf(stderr,"\n *** cannot allocate lmf_str (%ld) for %s\n",
@@ -480,7 +540,16 @@
| ~~~~~~~~~~~~~~~~~~~~~~
| |
| unsigned int
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c c_dispn.c
+initfa.c: In function 'alloc_pam2p':
+initfa.c:2001:39: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
+ 2001 | "Cannot reallocate pam2p[0]: %ld\n", (nsq+1)*len*sizeof(int));
+ | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~
+ | | |
+ | long int unsigned int
+ | %d
nmgetlib.c: In function 'sel_hacc_libstr_init':
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c ncbl2_mlib.c -o ncbl2_mlib.o
nmgetlib.c:2026:49: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
2026 | fprintf(stderr, "cannot allocate acc_hash[%ld]\n",hash_max*sizeof(int));
| ~~^ ~~~~~~~~~~~~~~~~~~~~
@@ -506,6 +575,7 @@
| | |
| long int unsigned int
| %d
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c lib_sel.c
nmgetlib.c: In function 'agetlib':
nmgetlib.c:621:2: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
621 | fgets(&lm_fd->lline[strlen(lm_fd->lline)],MAX_STR/2,lm_fd->libf);
@@ -637,6 +707,7 @@
nmgetlib.c:1465:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1465 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c url_subs.c
nmgetlib.c: In function 'vranlib':
nmgetlib.c:1492:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1492 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
@@ -654,6 +725,7 @@
nmgetlib.c:1570:2: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1570 | fgets(&lm_fd->lline[strlen(lm_fd->lline)],MAX_STR/2,lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+cc -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mrandom.o mrandom.c
nmgetlib.c:1572:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1572 | fgets(&lm_fd->lline[strlen(lm_fd->lline)-MAX_STR/2],MAX_STR/2,lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -673,9 +745,9 @@
nmgetlib.c:1672:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1672 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c ncbl2_mlib.c -o ncbl2_mlib.o
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c lib_sel.c
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c url_subs.c
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DSW_SSE2 -DSSEARCH initfa.c -o init_sw_sse.o
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSW_SSE2 -c dropgsw2.c -o dropgsw2_sse.o
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSW_SSE2 -c smith_waterman_sse2.c
ncbl2_mlib.c: In function 'ncbl2_getlibn':
ncbl2_mlib.c:1433:47: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1433 | " could not read sequence record: %s %lld %ld != %ld: %d\n",
@@ -697,7 +769,6 @@
| ~~~
| |
| size_t {aka unsigned int}
-cc -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mrandom.o mrandom.c
ncbl2_mlib.c:1593:72: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=]
1593 | fprintf(stderr, "*** error [%s:%d] malloc amb table error size %ld\n",
| ~~^
@@ -708,6 +779,7 @@
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| unsigned int
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c wm_align.c -o lwm_align.o
ncbl2_mlib.c: In function 'load_ncbl2':
ncbl2_mlib.c:810:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
810 | fread(title_str,(size_t)1,(size_t)title_len,ifile);
@@ -729,6 +801,7 @@
ncbl2_mlib.c:1840:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1840 | fread((char *)&b[0],(size_t)1,(size_t)4,fd);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSSEARCH -c cal_cons2.c -o calcons_sw.o
ncbl2_mlib.c: In function 'src_long4_read':
ncbl2_mlib.c:1855:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1855 | fread((char *)&b[0],(size_t)1,(size_t)4,fd);
@@ -753,12 +826,8 @@
ncbl2_mlib.c:1915:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1915 | fread(val,(size_t)slen,(size_t)1,fd);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DSW_SSE2 -DSSEARCH initfa.c -o init_sw_sse.o
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSW_SSE2 -c dropgsw2.c -o dropgsw2_sse.o
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSW_SSE2 -c smith_waterman_sse2.c
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c wm_align.c -o lwm_align.o
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSSEARCH -c cal_cons2.c -o calcons_sw.o
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c pssm_asn_subs.c
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DCOMP_MLIB -c comp_lib9.c -o comp_mlib9.o
initfa.c: In function 'alloc_pam2p':
initfa.c:2001:39: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
2001 | "Cannot reallocate pam2p[0]: %ld\n", (nsq+1)*len*sizeof(int));
@@ -766,9 +835,11 @@
| | |
| long int unsigned int
| %d
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DCOMP_MLIB -c comp_lib9.c -o comp_mlib9.o
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DCOMP_MLIB -c compacc2e.c -o compacc2_s.o
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DLALIGN -c mshowalign2.c -o lshowalign.o
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DLALIGN initfa.c -o init_lal.o
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c last_thresh.c
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -DLALIGN -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSW_SSE2 -c dropgsw2.c -o droplal2_sse.o
mshowalign2.c: In function 'showalign':
mshowalign2.c:614:57: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
614 | fprintf(stderr," mshowalign: nc/maxc: %d/%d seqc0/1: %lu/%lu\n",
@@ -790,10 +861,8 @@
| ~~~~~~~~~~~~~
| |
| size_t {aka unsigned int}
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DLALIGN initfa.c -o init_lal.o
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c last_thresh.c
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -DLALIGN -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSW_SSE2 -c dropgsw2.c -o droplal2_sse.o
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c lsim4.c
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -DLALIGN -DLCAL_CONS -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c cal_cons2.c -o calcons_la.o
initfa.c: In function 'alloc_pam2p':
initfa.c:2001:39: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
2001 | "Cannot reallocate pam2p[0]: %ld\n", (nsq+1)*len*sizeof(int));
@@ -801,7 +870,6 @@
| | |
| long int unsigned int
| %d
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -DLALIGN -DLCAL_CONS -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c cal_cons2.c -o calcons_la.o
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTS initfa.c -o init_fs.o
lsim4.c: In function 'ckalloc':
lsim4.c:994:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
@@ -826,13 +894,7 @@
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c last_tat.c
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTS tatstats.c -o tatstats_fs.o
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DFASTS -c dropfs2.c -o drop_fs2.o
-initfa.c: In function 'alloc_pam2p':
-initfa.c:2001:39: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
- 2001 | "Cannot reallocate pam2p[0]: %ld\n", (nsq+1)*len*sizeof(int));
- | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~
- | | |
- | long int unsigned int
- | %d
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DFASTS -c cal_consf.c -o calcons_fs.o
scaleswt.c: In function 'process_hist':
scaleswt.c:184:52: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
184 | fprintf(stderr," cannot allocate rs_snion: %ld\n",sizeof(struct pstat_str));
@@ -841,7 +903,16 @@
| | unsigned int
| long int
| %d
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTX initfa.c -o init_fx.o
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c faatran.c
+initfa.c: In function 'alloc_pam2p':
scaleswt.c: In function 'last_stats':
+initfa.c:2001:39: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
+ 2001 | "Cannot reallocate pam2p[0]: %ld\n", (nsq+1)*len*sizeof(int));
+ | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~
+ | | |
+ | long int unsigned int
+ | %d
scaleswt.c:1230:48: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
1230 | fprintf(stderr," cannot allocate rs_s: %ld\n",sizeof(struct pstat_str));
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~
@@ -849,7 +920,9 @@
| | unsigned int
| long int
| %d
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DFASTS -c cal_consf.c -o calcons_fs.o
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c dropfx2.c -o drop_fx.o
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTX -DTFAST initfa.c -o init_tfx.o
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DTFAST dropfx2.c -o drop_tfx.o
dropfs2.c: In function 'init_work':
dropfs2.c:377:61: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
377 | fprintf (stderr, " cannot allocate tatprobs array: %ld\n",
@@ -861,12 +934,17 @@
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| unsigned int
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTX initfa.c -o init_fx.o
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c faatran.c
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c dropfx2.c -o drop_fx.o
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTX -DTFAST initfa.c -o init_tfx.o
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DTFAST dropfx2.c -o drop_tfx.o
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTY initfa.c -o init_fy.o
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c dropfz3.c -o drop_fz.o
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTY -DTFAST initfa.c -o init_tfy.o
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DTFAST dropfz3.c -o drop_tfz.o
initfa.c: In function 'alloc_pam2p':
+initfa.c:2001:39: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
+ 2001 | "Cannot reallocate pam2p[0]: %ld\n", (nsq+1)*len*sizeof(int));
+ | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~
+ | | |
+ | long int unsigned int
+ | %d
dropfx2.c: In function 'do_walign':
dropfx2.c:2660:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'unsigned int' [-Wformat=]
2660 | fprintf(stderr,"*** error [%s:%d] - cannot allocate a_res [%lu]",
@@ -878,12 +956,7 @@
| ~~~~~~~~~~~~~~~~~~~~~~~~
| |
| unsigned int
-initfa.c:2001:39: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
- 2001 | "Cannot reallocate pam2p[0]: %ld\n", (nsq+1)*len*sizeof(int));
- | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~
- | | |
- | long int unsigned int
- | %d
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTS -DTFAST initfa.c -o init_tfs.o
initfa.c: In function 'alloc_pam2p':
initfa.c:2001:39: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
2001 | "Cannot reallocate pam2p[0]: %ld\n", (nsq+1)*len*sizeof(int));
@@ -891,9 +964,6 @@
| | |
| long int unsigned int
| %d
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTY initfa.c -o init_fy.o
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c dropfz3.c -o drop_fz.o
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTY -DTFAST initfa.c -o init_tfy.o
dropfx2.c: In function 'do_walign':
dropfx2.c:2660:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'unsigned int' [-Wformat=]
2660 | fprintf(stderr,"*** error [%s:%d] - cannot allocate a_res [%lu]",
@@ -905,15 +975,17 @@
| ~~~~~~~~~~~~~~~~~~~~~~~~
| |
| unsigned int
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DTFAST dropfz3.c -o drop_tfz.o
-initfa.c: In function 'alloc_pam2p':
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTS -DTFAST initfa.c -o init_tfs.o
-initfa.c:2001:39: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
- 2001 | "Cannot reallocate pam2p[0]: %ld\n", (nsq+1)*len*sizeof(int));
- | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~
- | | |
- | long int unsigned int
- | %d
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DTFAST -DFASTS dropfs2.c -o drop_tfs.o
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DTFAST -DFASTS -c cal_consf.c -o calcons_tfs.o
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTM initfa.c -o init_fm.o
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTM tatstats.c -o tatstats_fm.o
+dropfz3.c: In function 'init_work':
+dropfz3.c:629:79: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'unsigned int' [-Wformat=]
+ 629 | fprintf (stderr,"*** error [%s:%d] - cannot allocate diagonal arrays: %lu\n",
+ | ~~^
+ | |
+ | long unsigned int
+ | %u
dropfz3.c: In function 'init_work':
dropfz3.c:629:79: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'unsigned int' [-Wformat=]
629 | fprintf (stderr,"*** error [%s:%d] - cannot allocate diagonal arrays: %lu\n",
@@ -921,8 +993,14 @@
| |
| long unsigned int
| %u
-dropfz3.c: In function 'do_walign':
initfa.c: In function 'alloc_pam2p':
+initfa.c:2001:39: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
+ 2001 | "Cannot reallocate pam2p[0]: %ld\n", (nsq+1)*len*sizeof(int));
+ | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~
+ | | |
+ | long int unsigned int
+ | %d
+dropfz3.c: In function 'do_walign':
dropfz3.c:2672:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'unsigned int' [-Wformat=]
2672 | fprintf(stderr,"*** error [%s:%d] - cannot allocate a_res [%lu]",
| ~~^
@@ -933,21 +1011,15 @@
| ~~~~~~~~~~~~~~~~~~~~~~~~
| |
| unsigned int
+initfa.c: In function 'alloc_pam2p':
initfa.c:2001:39: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
2001 | "Cannot reallocate pam2p[0]: %ld\n", (nsq+1)*len*sizeof(int));
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long int unsigned int
| %d
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DTFAST -DFASTS dropfs2.c -o drop_tfs.o
-dropfz3.c: In function 'init_work':
-dropfz3.c:629:79: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'unsigned int' [-Wformat=]
- 629 | fprintf (stderr,"*** error [%s:%d] - cannot allocate diagonal arrays: %lu\n",
- | ~~^
- | |
- | long unsigned int
- | %u
dropfz3.c: In function 'do_walign':
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTM dropfs2.c -o drop_fm.o
dropfz3.c:2672:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'unsigned int' [-Wformat=]
2672 | fprintf(stderr,"*** error [%s:%d] - cannot allocate a_res [%lu]",
| ~~^
@@ -958,14 +1030,8 @@
| ~~~~~~~~~~~~~~~~~~~~~~~~
| |
| unsigned int
-initfa.c: In function 'alloc_pam2p':
-initfa.c:2001:39: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
- 2001 | "Cannot reallocate pam2p[0]: %ld\n", (nsq+1)*len*sizeof(int));
- | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~
- | | |
- | long int unsigned int
- | %d
dropfs2.c: In function 'init_work':
+initfa.c: In function 'alloc_pam2p':
dropfs2.c:377:61: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
377 | fprintf (stderr, " cannot allocate tatprobs array: %ld\n",
| ~~^
@@ -976,10 +1042,14 @@
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| unsigned int
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DTFAST -DFASTS -c cal_consf.c -o calcons_tfs.o
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTM initfa.c -o init_fm.o
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTM tatstats.c -o tatstats_fm.o
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTM dropfs2.c -o drop_fm.o
+initfa.c:2001:39: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
+ 2001 | "Cannot reallocate pam2p[0]: %ld\n", (nsq+1)*len*sizeof(int));
+ | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~
+ | | |
+ | long int unsigned int
+ | %d
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DFASTM -c cal_consf.c -o calcons_fm.o
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c mshowalign2.c -o mshowalign2_s.o
initfa.c: In function 'alloc_pam2p':
initfa.c:2001:39: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
2001 | "Cannot reallocate pam2p[0]: %ld\n", (nsq+1)*len*sizeof(int));
@@ -998,11 +1068,7 @@
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| unsigned int
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DFASTM -c cal_consf.c -o calcons_fm.o
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c mshowalign2.c -o mshowalign2_s.o
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTM -DTFAST initfa.c -o init_tfm.o
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DTFAST -DFASTM dropfs2.c -o drop_tfm.o
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DTFAST -DFASTM -c cal_consf.c -o calcons_tfm.o
mshowalign2.c: In function 'showalign':
mshowalign2.c:614:57: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
614 | fprintf(stderr," mshowalign: nc/maxc: %d/%d seqc0/1: %lu/%lu\n",
@@ -1024,7 +1090,16 @@
| ~~~~~~~~~~~~~
| |
| size_t {aka unsigned int}
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DTFAST -DFASTM dropfs2.c -o drop_tfm.o
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DTFAST -DFASTM -c cal_consf.c -o calcons_tfm.o
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTF initfa.c -o init_ff.o
+initfa.c: In function 'alloc_pam2p':
+initfa.c:2001:39: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
+ 2001 | "Cannot reallocate pam2p[0]: %ld\n", (nsq+1)*len*sizeof(int));
+ | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~
+ | | |
+ | long int unsigned int
+ | %d
dropfs2.c: In function 'init_work':
dropfs2.c:377:61: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
377 | fprintf (stderr, " cannot allocate tatprobs array: %ld\n",
@@ -1036,13 +1111,6 @@
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| unsigned int
-initfa.c: In function 'alloc_pam2p':
-initfa.c:2001:39: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
- 2001 | "Cannot reallocate pam2p[0]: %ld\n", (nsq+1)*len*sizeof(int));
- | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~
- | | |
- | long int unsigned int
- | %d
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DFASTF -c scaleswt.c -o scaleswtf.o
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTF tatstats.c -o tatstats_ff.o
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTF dropff2.c -o drop_ff2.o
@@ -1055,6 +1123,7 @@
| | |
| long int unsigned int
| %d
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTF -DTFAST dropff2.c -o drop_tff.o
scaleswt.c: In function 'process_hist':
scaleswt.c:184:52: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
184 | fprintf(stderr," cannot allocate rs_snion: %ld\n",sizeof(struct pstat_str));
@@ -1063,6 +1132,8 @@
| | unsigned int
| long int
| %d
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DTFAST -DFASTF -c cal_consf.c -o calcons_tff.o
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -DNORMAL_DIST -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c scaleswn.c -o scale_sn.o
scaleswt.c: In function 'last_stats':
scaleswt.c:1230:48: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
1230 | fprintf(stderr," cannot allocate rs_s: %ld\n",sizeof(struct pstat_str));
@@ -1071,7 +1142,6 @@
| | unsigned int
| long int
| %d
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTF -DTFAST dropff2.c -o drop_tff.o
dropff2.c: In function 'init_work':
dropff2.c:120:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'unsigned int' [-Wformat=]
120 | fprintf(stderr, "*** error [%s:%d] - cannot calloc f_str [%lu]\n",
@@ -1083,6 +1153,7 @@
| ~~~~~~~~~~~~~~~~~~~~~~~
| |
| unsigned int
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DSW_SSE2 -DGLSEARCH initfa.c -o init_lnw_sse.o
dropff2.c: In function 'do_walign':
dropff2.c:1176:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'unsigned int' [-Wformat=]
1176 | fprintf(stderr,"*** error [%s:%d] - cannot allocate a_res [%lu]",
@@ -1094,13 +1165,9 @@
| ~~~~~~~~~~~~~~~~~~~~~~~~
| |
| unsigned int
-initfa.c: In function 'alloc_pam2p':
-initfa.c:2001:39: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
- 2001 | "Cannot reallocate pam2p[0]: %ld\n", (nsq+1)*len*sizeof(int));
- | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~
- | | |
- | long int unsigned int
- | %d
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -DSW_SSE2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c dropnnw2.c -o droplnw_sse.o
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSW_SSE2 -c glocal_sse2.c
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DGGSEARCH -c wm_align.c -o gwm_align.o
dropff2.c: In function 'init_work':
dropff2.c:120:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'unsigned int' [-Wformat=]
120 | fprintf(stderr, "*** error [%s:%d] - cannot calloc f_str [%lu]\n",
@@ -1112,7 +1179,14 @@
| ~~~~~~~~~~~~~~~~~~~~~~~
| |
| unsigned int
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DTFAST -DFASTF -c cal_consf.c -o calcons_tff.o
+scaleswn.c: In function 'process_hist':
+scaleswn.c:255:55: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
+ 255 | fprintf(stderr," cannot allocate pstat_union: %ld\n",sizeof(struct pstat_str));
+ | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~
+ | | |
+ | | unsigned int
+ | long int
+ | %d
dropff2.c: In function 'do_walign':
dropff2.c:1176:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'unsigned int' [-Wformat=]
1176 | fprintf(stderr,"*** error [%s:%d] - cannot allocate a_res [%lu]",
@@ -1124,19 +1198,6 @@
| ~~~~~~~~~~~~~~~~~~~~~~~~
| |
| unsigned int
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -DNORMAL_DIST -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c scaleswn.c -o scale_sn.o
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DSW_SSE2 -DGLSEARCH initfa.c -o init_lnw_sse.o
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -DSW_SSE2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c dropnnw2.c -o droplnw_sse.o
-scaleswn.c: In function 'process_hist':
-scaleswn.c:255:55: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
- 255 | fprintf(stderr," cannot allocate pstat_union: %ld\n",sizeof(struct pstat_str));
- | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~
- | | |
- | | unsigned int
- | long int
- | %d
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSW_SSE2 -c glocal_sse2.c
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DGGSEARCH -c wm_align.c -o gwm_align.o
initfa.c: In function 'alloc_pam2p':
initfa.c:2001:39: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
2001 | "Cannot reallocate pam2p[0]: %ld\n", (nsq+1)*len*sizeof(int));
@@ -1145,18 +1206,19 @@
| long int unsigned int
| %d
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DSW_SSE2 -DGGSEARCH initfa.c -o init_gnw_sse.o
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -DGLOBAL_GLOBAL -DSW_SSE2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c dropnnw2.c -o dropgnw_sse.o
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSW_SSE2 -c global_sse2.c
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -o ../bin/map_db map_db.c
initfa.c: In function 'alloc_pam2p':
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/fasta36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fa.o drop_nfa.o wm_align.o calcons_fa.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o -lm -lpthread
initfa.c:2001:39: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
2001 | "Cannot reallocate pam2p[0]: %ld\n", (nsq+1)*len*sizeof(int));
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long int unsigned int
| %d
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -DGLOBAL_GLOBAL -DSW_SSE2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c dropnnw2.c -o dropgnw_sse.o
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSW_SSE2 -c global_sse2.c
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -o ../bin/map_db map_db.c
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/fasta36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fa.o drop_nfa.o wm_align.o calcons_fa.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o -lm -lpthread
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/ssearch36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_sw_sse.o dropgsw2_sse.o smith_waterman_sse2.o lwm_align.o calcons_sw.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lpthread
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/lalign36 comp_mlib9.o compacc2_s.o showbest.o build_ares.o re_getlib.o lshowalign.o htime.o apam.o doinit.o init_lal.o droplal2_sse.o smith_waterman_sse2.o lsim4.o calcons_la.o scale_se.o karlin.o last_thresh.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm
map_db.c: In function 'main':
map_db.c:149:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
149 | fgets(lname,sizeof(lname),stdin);
@@ -1169,13 +1231,18 @@
map_db.c:524:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
524 | fread((char *)&b[0],(size_t)1,(size_t)4,fd);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/lalign36 comp_mlib9.o compacc2_s.o showbest.o build_ares.o re_getlib.o lshowalign.o htime.o apam.o doinit.o init_lal.o droplal2_sse.o smith_waterman_sse2.o lsim4.o calcons_la.o scale_se.o karlin.o last_thresh.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm
+initfa.c: In function 'alloc_pam2p':
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/fasts36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fs.o drop_fs2.o calcons_fs.o scaleswts.o last_tat.o tatstats_fs.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o mrandom.o url_subs.o -lm -lpthread
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/fastx36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fx.o drop_fx.o faatran.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o -lm -lpthread
+initfa.c:2001:39: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
+ 2001 | "Cannot reallocate pam2p[0]: %ld\n", (nsq+1)*len*sizeof(int));
+ | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~
+ | | |
+ | long int unsigned int
+ | %d
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/tfastx36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tfx.o drop_tfx.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o url_subs.o mrandom.o -lm -lpthread
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/fasty36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fy.o drop_fz.o faatran.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o -lm -lpthread
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/tfasty36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tfy.o drop_tfz.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o url_subs.o mrandom.o -lm -lpthread
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/tfasts36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tfs.o drop_tfs.o calcons_tfs.o scaleswts.o last_tat.o tatstats_fs.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o mrandom.o url_subs.o -lm -lpthread
compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch]
954 | re_openlib(struct lmf_str *, int outtty);
| ^
@@ -1192,6 +1259,13 @@
| ^
compacc2e.c:2290:1: note: 's_annot_to_aa1a' was previously declared here
compacc2e.c:2290:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
+comp_lib9.c:250:5: warning: type of 'last_calc' does not match original declaration [-Wlto-type-mismatch]
+ 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn,
+ | ^
+initfa.c:2036:1: note: type mismatch in parameter 6
+ 2036 | last_calc(
+ | ^
+initfa.c:2036:1: note: 'last_calc' was previously declared here
mshowbest.c:82:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch]
82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p,
| ^
@@ -1203,13 +1277,14 @@
comp_lib9.c:287:1: warning: type of 'showalign' does not match original declaration [-Wlto-type-mismatch]
287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn,
| ^
-compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch]
- 954 | re_openlib(struct lmf_str *, int outtty);
- | ^
mshowalign2.c:134:6: note: 'showalign' was previously declared here
134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn,
| ^
mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/tfasts36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tfs.o drop_tfs.o calcons_tfs.o scaleswts.o last_tat.o tatstats_fs.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o mrandom.o url_subs.o -lm -lpthread
+compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch]
+ 954 | re_openlib(struct lmf_str *, int outtty);
+ | ^
nmgetlib.c:503:3: note: type mismatch in parameter 2
503 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty)
| ^
@@ -1218,19 +1293,35 @@
mshowbest.c:63:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch]
63 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr);
| ^
+compacc2e.c:2290:1: note: type mismatch in parameter 2
+ 2290 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) {
+ | ^
+compacc2e.c:2290:1: note: 's_annot_to_aa1a' was previously declared here
+compacc2e.c:2290:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
+mshowbest.c:82:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch]
+ 82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p,
+ | ^
+compacc2e.c:2178:1: note: type mismatch in parameter 5
+ 2178 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, long offset, int n1, struct annot_str **annot_p,
+ | ^
+compacc2e.c:2178:1: note: 'get_annot' was previously declared here
+compacc2e.c:2178:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
+comp_lib9.c:287:1: warning: type of 'showalign' does not match original declaration [-Wlto-type-mismatch]
+ 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn,
+ | ^
+mshowalign2.c:134:6: note: 'showalign' was previously declared here
+ 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn,
+ | ^
+mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/fastm36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fm.o drop_fm.o calcons_fm.o scaleswts.o last_tat.o tatstats_fm.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o mrandom.o url_subs.o -lm -lpthread
compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch]
954 | re_openlib(struct lmf_str *, int outtty);
| ^
nmgetlib.c:503:3: note: type mismatch in parameter 2
503 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty)
| ^
-compacc2e.c:2290:1: note: type mismatch in parameter 2
- 2290 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) {
- | ^
nmgetlib.c:503:3: note: 're_openlib' was previously declared here
-compacc2e.c:2290:1: note: 's_annot_to_aa1a' was previously declared here
nmgetlib.c:503:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used
-compacc2e.c:2290:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
mshowbest.c:63:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch]
63 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr);
| ^
@@ -1242,9 +1333,6 @@
comp_lib9.c:250:5: warning: type of 'last_calc' does not match original declaration [-Wlto-type-mismatch]
250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn,
| ^
-comp_lib9.c:250:5: warning: type of 'last_calc' does not match original declaration [-Wlto-type-mismatch]
- 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn,
- | ^
initfa.c:2036:1: note: type mismatch in parameter 6
2036 | last_calc(
| ^
@@ -1260,14 +1348,73 @@
comp_lib9.c:287:1: warning: type of 'showalign' does not match original declaration [-Wlto-type-mismatch]
287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn,
| ^
+mshowalign2.c:134:6: note: 'showalign' was previously declared here
+ 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn,
+ | ^
+mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/tfastm36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_s.o htime.o apam.o doinit.o init_tfm.o drop_tfm.o calcons_tfm.o scaleswts.o tatstats_fm.o last_tat.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o mrandom.o url_subs.o -lm -lpthread
+compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch]
+ 954 | re_openlib(struct lmf_str *, int outtty);
+ | ^
+nmgetlib.c:503:3: note: type mismatch in parameter 2
+ 503 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty)
+ | ^
+nmgetlib.c:503:3: note: 're_openlib' was previously declared here
+nmgetlib.c:503:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used
+mshowbest.c:63:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch]
+ 63 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr);
+ | ^
+compacc2e.c:2290:1: note: type mismatch in parameter 2
+ 2290 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) {
+ | ^
+compacc2e.c:2290:1: note: 's_annot_to_aa1a' was previously declared here
+compacc2e.c:2290:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
+comp_lib9.c:250:5: warning: type of 'last_calc' does not match original declaration [-Wlto-type-mismatch]
+ 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn,
+ | ^
initfa.c:2036:1: note: type mismatch in parameter 6
2036 | last_calc(
| ^
initfa.c:2036:1: note: 'last_calc' was previously declared here
+mshowbest.c:82:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch]
+ 82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p,
+ | ^
+compacc2e.c:2178:1: note: type mismatch in parameter 5
+ 2178 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, long offset, int n1, struct annot_str **annot_p,
+ | ^
+compacc2e.c:2178:1: note: 'get_annot' was previously declared here
+compacc2e.c:2178:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
+comp_lib9.c:287:1: warning: type of 'showalign' does not match original declaration [-Wlto-type-mismatch]
+ 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn,
+ | ^
mshowalign2.c:134:6: note: 'showalign' was previously declared here
134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn,
| ^
mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used
+compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch]
+ 954 | re_openlib(struct lmf_str *, int outtty);
+ | ^
+nmgetlib.c:503:3: note: type mismatch in parameter 2
+ 503 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty)
+ | ^
+nmgetlib.c:503:3: note: 're_openlib' was previously declared here
+nmgetlib.c:503:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used
+mshowbest.c:63:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch]
+ 63 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr);
+ | ^
+compacc2e.c:2290:1: note: type mismatch in parameter 2
+ 2290 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) {
+ | ^
+compacc2e.c:2290:1: note: 's_annot_to_aa1a' was previously declared here
+compacc2e.c:2290:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
+comp_lib9.c:236:1: warning: type of 'process_hist' does not match original declaration [-Wlto-type-mismatch]
+ 236 | process_hist(struct stat_str *sptr, int nstats,
+ | ^
+scaleswt.c:164:1: note: type mismatch in parameter 7
+ 164 | process_hist(struct stat_str *sptr, int nstats,
+ | ^
+scaleswt.c:164:1: note: 'process_hist' was previously declared here
+scaleswt.c:164:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
mshowbest.c:82:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch]
82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p,
| ^
@@ -1276,9 +1423,6 @@
| ^
compacc2e.c:2178:1: note: 'get_annot' was previously declared here
compacc2e.c:2178:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
-compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch]
- 954 | re_openlib(struct lmf_str *, int outtty);
- | ^
comp_lib9.c:287:1: warning: type of 'showalign' does not match original declaration [-Wlto-type-mismatch]
287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn,
| ^
@@ -1286,6 +1430,9 @@
134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn,
| ^
mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used
+compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch]
+ 954 | re_openlib(struct lmf_str *, int outtty);
+ | ^
nmgetlib.c:503:3: note: type mismatch in parameter 2
503 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty)
| ^
@@ -1294,14 +1441,74 @@
mshowbest.c:63:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch]
63 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr);
| ^
+compacc2e.c:2290:1: note: type mismatch in parameter 2
+ 2290 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) {
+ | ^
+compacc2e.c:2290:1: note: 's_annot_to_aa1a' was previously declared here
+compacc2e.c:2290:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
+comp_lib9.c:250:5: warning: type of 'last_calc' does not match original declaration [-Wlto-type-mismatch]
+ 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn,
+ | ^
+initfa.c:2036:1: note: type mismatch in parameter 6
+ 2036 | last_calc(
+ | ^
+initfa.c:2036:1: note: 'last_calc' was previously declared here
+mshowbest.c:82:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch]
+ 82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p,
+ | ^
+compacc2e.c:2178:1: note: type mismatch in parameter 5
+ 2178 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, long offset, int n1, struct annot_str **annot_p,
+ | ^
+compacc2e.c:2178:1: note: 'get_annot' was previously declared here
+compacc2e.c:2178:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
+comp_lib9.c:287:1: warning: type of 'showalign' does not match original declaration [-Wlto-type-mismatch]
+ 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn,
+ | ^
+mshowalign2.c:134:6: note: 'showalign' was previously declared here
+ 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn,
+ | ^
+mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used
compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch]
954 | re_openlib(struct lmf_str *, int outtty);
| ^
+nmgetlib.c:503:3: note: type mismatch in parameter 2
+ 503 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty)
+ | ^
+nmgetlib.c:503:3: note: 're_openlib' was previously declared here
+nmgetlib.c:503:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used
+mshowbest.c:63:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch]
+ 63 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr);
+ | ^
compacc2e.c:2290:1: note: type mismatch in parameter 2
2290 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) {
| ^
compacc2e.c:2290:1: note: 's_annot_to_aa1a' was previously declared here
compacc2e.c:2290:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
+comp_lib9.c:250:5: warning: type of 'last_calc' does not match original declaration [-Wlto-type-mismatch]
+ 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn,
+ | ^
+initfa.c:2036:1: note: type mismatch in parameter 6
+ 2036 | last_calc(
+ | ^
+initfa.c:2036:1: note: 'last_calc' was previously declared here
+mshowbest.c:82:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch]
+ 82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p,
+ | ^
+compacc2e.c:2178:1: note: type mismatch in parameter 5
+ 2178 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, long offset, int n1, struct annot_str **annot_p,
+ | ^
+compacc2e.c:2178:1: note: 'get_annot' was previously declared here
+compacc2e.c:2178:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
+comp_lib9.c:287:1: warning: type of 'showalign' does not match original declaration [-Wlto-type-mismatch]
+ 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn,
+ | ^
+mshowalign2.c:134:6: note: 'showalign' was previously declared here
+ 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn,
+ | ^
+mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used
+compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch]
+ 954 | re_openlib(struct lmf_str *, int outtty);
+ | ^
nmgetlib.c:503:3: note: type mismatch in parameter 2
503 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty)
| ^
@@ -1322,9 +1529,6 @@
2036 | last_calc(
| ^
initfa.c:2036:1: note: 'last_calc' was previously declared here
-comp_lib9.c:236:1: warning: type of 'process_hist' does not match original declaration [-Wlto-type-mismatch]
- 236 | process_hist(struct stat_str *sptr, int nstats,
- | ^
mshowbest.c:82:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch]
82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p,
| ^
@@ -1336,6 +1540,30 @@
comp_lib9.c:287:1: warning: type of 'showalign' does not match original declaration [-Wlto-type-mismatch]
287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn,
| ^
+mshowalign2.c:134:6: note: 'showalign' was previously declared here
+ 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn,
+ | ^
+mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/fastf36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_ff.o drop_ff2.o calcons_ff.o scaleswtf.o last_tat.o tatstats_ff.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o mrandom.o url_subs.o -lm -lpthread
+compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch]
+ 954 | re_openlib(struct lmf_str *, int outtty);
+ | ^
+nmgetlib.c:503:3: note: type mismatch in parameter 2
+ 503 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty)
+ | ^
+nmgetlib.c:503:3: note: 're_openlib' was previously declared here
+nmgetlib.c:503:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used
+mshowbest.c:63:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch]
+ 63 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr);
+ | ^
+compacc2e.c:2290:1: note: type mismatch in parameter 2
+ 2290 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) {
+ | ^
+compacc2e.c:2290:1: note: 's_annot_to_aa1a' was previously declared here
+compacc2e.c:2290:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
+comp_lib9.c:236:1: warning: type of 'process_hist' does not match original declaration [-Wlto-type-mismatch]
+ 236 | process_hist(struct stat_str *sptr, int nstats,
+ | ^
scaleswt.c:164:1: note: type mismatch in parameter 7
164 | process_hist(struct stat_str *sptr, int nstats,
| ^
@@ -1344,13 +1572,48 @@
mshowbest.c:82:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch]
82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p,
| ^
+compacc2e.c:2178:1: note: type mismatch in parameter 5
+ 2178 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, long offset, int n1, struct annot_str **annot_p,
+ | ^
+compacc2e.c:2178:1: note: 'get_annot' was previously declared here
+compacc2e.c:2178:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
+comp_lib9.c:287:1: warning: type of 'showalign' does not match original declaration [-Wlto-type-mismatch]
+ 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn,
+ | ^
mshowalign2.c:134:6: note: 'showalign' was previously declared here
134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn,
| ^
+mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used
+compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch]
+ 954 | re_openlib(struct lmf_str *, int outtty);
+ | ^
+nmgetlib.c:503:3: note: type mismatch in parameter 2
+ 503 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty)
+ | ^
+nmgetlib.c:503:3: note: 're_openlib' was previously declared here
+nmgetlib.c:503:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used
+mshowbest.c:63:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch]
+ 63 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr);
+ | ^
+compacc2e.c:2290:1: note: type mismatch in parameter 2
+ 2290 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) {
+ | ^
+compacc2e.c:2290:1: note: 's_annot_to_aa1a' was previously declared here
+compacc2e.c:2290:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
+comp_lib9.c:236:1: warning: type of 'process_hist' does not match original declaration [-Wlto-type-mismatch]
+ 236 | process_hist(struct stat_str *sptr, int nstats,
+ | ^
+scaleswt.c:164:1: note: type mismatch in parameter 7
+ 164 | process_hist(struct stat_str *sptr, int nstats,
+ | ^
+scaleswt.c:164:1: note: 'process_hist' was previously declared here
+scaleswt.c:164:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
+mshowbest.c:82:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch]
+ 82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p,
+ | ^
compacc2e.c:2178:1: note: type mismatch in parameter 5
2178 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, long offset, int n1, struct annot_str **annot_p,
| ^
-mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used
compacc2e.c:2178:1: note: 'get_annot' was previously declared here
compacc2e.c:2178:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
comp_lib9.c:287:1: warning: type of 'showalign' does not match original declaration [-Wlto-type-mismatch]
@@ -1360,6 +1623,7 @@
134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn,
| ^
mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/tfastf36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tf.o drop_tff.o calcons_tff.o scaleswtf.o last_tat.o tatstats_ff.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o mrandom.o url_subs.o -lm -lpthread
compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch]
954 | re_openlib(struct lmf_str *, int outtty);
| ^
@@ -1376,13 +1640,14 @@
| ^
compacc2e.c:2290:1: note: 's_annot_to_aa1a' was previously declared here
compacc2e.c:2290:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
-comp_lib9.c:250:5: warning: type of 'last_calc' does not match original declaration [-Wlto-type-mismatch]
- 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn,
- | ^
-initfa.c:2036:1: note: type mismatch in parameter 6
- 2036 | last_calc(
+comp_lib9.c:236:1: warning: type of 'process_hist' does not match original declaration [-Wlto-type-mismatch]
+ 236 | process_hist(struct stat_str *sptr, int nstats,
| ^
-initfa.c:2036:1: note: 'last_calc' was previously declared here
+scaleswt.c:164:1: note: type mismatch in parameter 7
+ 164 | process_hist(struct stat_str *sptr, int nstats,
+ | ^
+scaleswt.c:164:1: note: 'process_hist' was previously declared here
+scaleswt.c:164:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
mshowbest.c:82:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch]
82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p,
| ^
@@ -1391,6 +1656,13 @@
| ^
compacc2e.c:2178:1: note: 'get_annot' was previously declared here
compacc2e.c:2178:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
+mshowalign2.c:85:1: warning: type of 'buf_align_seq' does not match original declaration [-Wlto-type-mismatch]
+ 85 | buf_align_seq(unsigned char **aa0, int n0,
+ | ^
+compacc2e.c:3575:1: note: type mismatch in parameter 8
+ 3575 | buf_align_seq(unsigned char **aa0, int n0,
+ | ^
+compacc2e.c:3575:1: note: 'buf_align_seq' was previously declared here
comp_lib9.c:287:1: warning: type of 'showalign' does not match original declaration [-Wlto-type-mismatch]
287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn,
| ^
@@ -1453,13 +1725,14 @@
| ^
compacc2e.c:2290:1: note: 's_annot_to_aa1a' was previously declared here
compacc2e.c:2290:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
-comp_lib9.c:250:5: warning: type of 'last_calc' does not match original declaration [-Wlto-type-mismatch]
- 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn,
- | ^
-initfa.c:2036:1: note: type mismatch in parameter 6
- 2036 | last_calc(
+comp_lib9.c:236:1: warning: type of 'process_hist' does not match original declaration [-Wlto-type-mismatch]
+ 236 | process_hist(struct stat_str *sptr, int nstats,
| ^
-initfa.c:2036:1: note: 'last_calc' was previously declared here
+scaleswt.c:164:1: note: type mismatch in parameter 7
+ 164 | process_hist(struct stat_str *sptr, int nstats,
+ | ^
+scaleswt.c:164:1: note: 'process_hist' was previously declared here
+scaleswt.c:164:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
mshowbest.c:82:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch]
82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p,
| ^
@@ -1475,6 +1748,8 @@
134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn,
| ^
mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/glsearch36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_lnw_sse.o droplnw_sse.o glocal_sse2.o gwm_align.o calcons_sw.o scale_sn.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lpthread
+cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/ggsearch36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_gnw_sse.o dropgnw_sse.o global_sse2.o gwm_align.o calcons_sw.o scale_sn.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lpthread
compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch]
954 | re_openlib(struct lmf_str *, int outtty);
| ^
@@ -1513,7 +1788,6 @@
134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn,
| ^
mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/fastm36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fm.o drop_fm.o calcons_fm.o scaleswts.o last_tat.o tatstats_fm.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o mrandom.o url_subs.o -lm -lpthread
compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch]
954 | re_openlib(struct lmf_str *, int outtty);
| ^
@@ -1530,14 +1804,13 @@
| ^
compacc2e.c:2290:1: note: 's_annot_to_aa1a' was previously declared here
compacc2e.c:2290:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
-comp_lib9.c:236:1: warning: type of 'process_hist' does not match original declaration [-Wlto-type-mismatch]
- 236 | process_hist(struct stat_str *sptr, int nstats,
- | ^
-scaleswt.c:164:1: note: type mismatch in parameter 7
- 164 | process_hist(struct stat_str *sptr, int nstats,
+comp_lib9.c:250:5: warning: type of 'last_calc' does not match original declaration [-Wlto-type-mismatch]
+ 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn,
+ | ^
+initfa.c:2036:1: note: type mismatch in parameter 6
+ 2036 | last_calc(
| ^
-scaleswt.c:164:1: note: 'process_hist' was previously declared here
-scaleswt.c:164:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
+initfa.c:2036:1: note: 'last_calc' was previously declared here
mshowbest.c:82:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch]
82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p,
| ^
@@ -1563,15 +1836,6 @@
217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2);
| ^
In function 'strncpy',
- inlined from 'add_annot_def' at doinit.c:627:7:
-/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
- 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
- | ^
-doinit.c: In function 'add_annot_def':
-doinit.c:627:7: note: length computed here
- 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1));
- | ^
-In function 'strncpy',
inlined from 'build_ares_code' at build_ares.c:217:4:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
@@ -1617,32 +1881,23 @@
627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1));
| ^
In function 'strncpy',
- inlined from 'add_annot_def' at doinit.c:627:7:
-/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
- 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
- | ^
-doinit.c: In function 'add_annot_def':
-doinit.c:627:7: note: length computed here
- 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1));
- | ^
-In function 'strncpy',
- inlined from 'add_annot_def' at doinit.c:627:7:
+ inlined from 'build_ares_code' at build_ares.c:217:4:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
-doinit.c: In function 'add_annot_def':
-doinit.c:627:7: note: length computed here
- 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1));
- | ^
+build_ares.c: In function 'build_ares_code':
+build_ares.c:217:59: note: length computed here
+ 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2);
+ | ^
In function 'strncpy',
- inlined from 'add_annot_def' at doinit.c:627:7:
+ inlined from 'build_ares_code' at build_ares.c:217:4:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
-doinit.c: In function 'add_annot_def':
-doinit.c:627:7: note: length computed here
- 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1));
- | ^
+build_ares.c: In function 'build_ares_code':
+build_ares.c:217:59: note: length computed here
+ 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2);
+ | ^
In function 'strncpy',
inlined from 'set_opt_disp_defs' at doinit.c:991:4,
inlined from 'f_init_opts' at initfa.c:476:3,
@@ -1725,6 +1980,69 @@
627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1));
| ^
In function 'strncpy',
+ inlined from 'add_annot_def' at doinit.c:627:7:
+/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
+ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
+ | ^
+doinit.c: In function 'add_annot_def':
+doinit.c:627:7: note: length computed here
+ 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1));
+ | ^
+In function 'strncpy',
+ inlined from 'add_annot_def' at doinit.c:627:7:
+/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
+ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
+ | ^
+doinit.c: In function 'add_annot_def':
+doinit.c:627:7: note: length computed here
+ 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1));
+ | ^
+In function 'strncpy',
+ inlined from 'add_annot_def' at doinit.c:627:7:
+/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
+ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
+ | ^
+doinit.c: In function 'add_annot_def':
+doinit.c:627:7: note: length computed here
+ 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1));
+ | ^
+In function 'strncpy',
+ inlined from 'add_annot_def' at doinit.c:627:7:
+/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
+ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
+ | ^
+doinit.c: In function 'add_annot_def':
+doinit.c:627:7: note: length computed here
+ 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1));
+ | ^
+In function 'strncpy',
+ inlined from 'add_annot_def' at doinit.c:627:7:
+/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
+ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
+ | ^
+doinit.c: In function 'add_annot_def':
+doinit.c:627:7: note: length computed here
+ 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1));
+ | ^
+In function 'strncpy',
+ inlined from 'add_annot_def' at doinit.c:627:7:
+/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
+ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
+ | ^
+doinit.c: In function 'add_annot_def':
+doinit.c:627:7: note: length computed here
+ 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1));
+ | ^
+In function 'strncpy',
+ inlined from 'add_annot_def' at doinit.c:627:7:
+/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
+ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
+ | ^
+doinit.c: In function 'add_annot_def':
+doinit.c:627:7: note: length computed here
+ 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1));
+ | ^
+In function 'strncpy',
inlined from 'set_opt_disp_defs' at doinit.c:991:4,
inlined from 'f_init_opts' at initfa.c:476:3,
inlined from 'f_initenv' at initfa.c:985:3,
@@ -1754,6 +2072,45 @@
inlined from 'f_initenv' at initfa.c:985:3,
inlined from 'initenv' at doinit.c:359:4,
inlined from 'main' at comp_lib9.c:576:3:
+In function 'strncpy',
+ inlined from 'set_opt_disp_defs' at doinit.c:991:4,
+ inlined from 'f_init_opts' at initfa.c:476:3,
+ inlined from 'f_initenv' at initfa.c:985:3,
+ inlined from 'initenv' at doinit.c:359:4,
+ inlined from 'main' at comp_lib9.c:576:3:
+/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
+ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
+ | ^
+/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
+ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
+ | ^
+comp_lib9.c: In function 'main':
+comp_lib9.c: In function 'main':
+doinit.c:991:4: note: length computed here
+ 991 | strncpy(this_opt->s_param,s_param,strlen(s_param));
+ | ^
+doinit.c:991:4: note: length computed here
+ 991 | strncpy(this_opt->s_param,s_param,strlen(s_param));
+ | ^
+In function 'strncpy',
+ inlined from 'set_opt_disp_defs' at doinit.c:991:4,
+ inlined from 'f_init_opts' at initfa.c:476:3,
+ inlined from 'f_initenv' at initfa.c:985:3,
+ inlined from 'initenv' at doinit.c:359:4,
+ inlined from 'main' at comp_lib9.c:576:3:
+/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
+ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
+ | ^
+comp_lib9.c: In function 'main':
+doinit.c:991:4: note: length computed here
+ 991 | strncpy(this_opt->s_param,s_param,strlen(s_param));
+ | ^
+In function 'strncpy',
+ inlined from 'set_opt_disp_defs' at doinit.c:991:4,
+ inlined from 'f_init_opts' at initfa.c:476:3,
+ inlined from 'f_initenv' at initfa.c:985:3,
+ inlined from 'initenv' at doinit.c:359:4,
+ inlined from 'main' at comp_lib9.c:576:3:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
@@ -1765,6 +2122,39 @@
inlined from 'pre_parse_markx' at doinit.c:785:5,
inlined from 'initenv' at doinit.c:402:4,
inlined from 'main' at comp_lib9.c:576:3:
+In function 'strncpy',
+ inlined from 'pre_parse_markx' at doinit.c:785:5,
+ inlined from 'initenv' at doinit.c:402:4,
+ inlined from 'main' at comp_lib9.c:576:3:
+/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
+ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
+ | ^
+/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
+ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
+ | ^
+comp_lib9.c: In function 'main':
+comp_lib9.c: In function 'main':
+doinit.c:785:5: note: length computed here
+ 785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1));
+ | ^
+doinit.c:785:5: note: length computed here
+ 785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1));
+ | ^
+In function 'strncpy',
+ inlined from 'pre_parse_markx' at doinit.c:785:5,
+ inlined from 'initenv' at doinit.c:402:4,
+ inlined from 'main' at comp_lib9.c:576:3:
+/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
+ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
+ | ^
+comp_lib9.c: In function 'main':
+doinit.c:785:5: note: length computed here
+ 785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1));
+ | ^
+In function 'strncpy',
+ inlined from 'pre_parse_markx' at doinit.c:785:5,
+ inlined from 'initenv' at doinit.c:402:4,
+ inlined from 'main' at comp_lib9.c:576:3:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
@@ -1858,6 +2248,30 @@
991 | strncpy(this_opt->s_param,s_param,strlen(s_param));
| ^
In function 'strncpy',
+ inlined from 'set_opt_disp_defs' at doinit.c:991:4,
+ inlined from 'f_init_opts' at initfa.c:476:3,
+ inlined from 'f_initenv' at initfa.c:985:3,
+ inlined from 'initenv' at doinit.c:359:4,
+ inlined from 'main' at comp_lib9.c:576:3:
+/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
+ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
+ | ^
+comp_lib9.c: In function 'main':
+doinit.c:991:4: note: length computed here
+ 991 | strncpy(this_opt->s_param,s_param,strlen(s_param));
+ | ^
+In function 'strncpy',
+ inlined from 'pre_parse_markx' at doinit.c:785:5,
+ inlined from 'initenv' at doinit.c:402:4,
+ inlined from 'main' at comp_lib9.c:576:3:
+/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
+ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
+ | ^
+comp_lib9.c: In function 'main':
+doinit.c:785:5: note: length computed here
+ 785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1));
+ | ^
+In function 'strncpy',
inlined from 'pre_parse_markx' at doinit.c:785:5,
inlined from 'initenv' at doinit.c:402:4,
inlined from 'main' at comp_lib9.c:576:3:
@@ -1893,23 +2307,29 @@
785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1));
| ^
In function 'strncpy',
- inlined from 'add_annot_def' at doinit.c:627:7:
+ inlined from 'set_opt_disp_defs' at doinit.c:991:4,
+ inlined from 'f_init_opts' at initfa.c:476:3,
+ inlined from 'f_initenv' at initfa.c:985:3,
+ inlined from 'initenv' at doinit.c:359:4,
+ inlined from 'main' at comp_lib9.c:576:3:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
-doinit.c: In function 'add_annot_def':
-doinit.c:627:7: note: length computed here
- 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1));
- | ^
+comp_lib9.c: In function 'main':
+doinit.c:991:4: note: length computed here
+ 991 | strncpy(this_opt->s_param,s_param,strlen(s_param));
+ | ^
In function 'strncpy',
- inlined from 'add_annot_def' at doinit.c:627:7:
+ inlined from 'pre_parse_markx' at doinit.c:785:5,
+ inlined from 'initenv' at doinit.c:402:4,
+ inlined from 'main' at comp_lib9.c:576:3:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
-doinit.c: In function 'add_annot_def':
-doinit.c:627:7: note: length computed here
- 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1));
- | ^
+comp_lib9.c: In function 'main':
+doinit.c:785:5: note: length computed here
+ 785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1));
+ | ^
In function 'strncpy',
inlined from 'add_annot_def' at doinit.c:627:7:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
@@ -1940,33 +2360,40 @@
2267 | fn_len = strlen(f_name);
| ^
In function 'strncpy',
- inlined from 'alloc_file_name' at nmgetlib.c:2274:5,
- inlined from 'open_lib' at nmgetlib.c:390:26:
+ inlined from 'add_annot_def' at doinit.c:627:7:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
-nmgetlib.c: In function 'open_lib':
-nmgetlib.c:2267:12: note: length computed here
- 2267 | fn_len = strlen(f_name);
- | ^
+doinit.c: In function 'add_annot_def':
+doinit.c:627:7: note: length computed here
+ 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1));
+ | ^
In function 'strncpy',
- inlined from 'alloc_file_name' at nmgetlib.c:2274:5,
- inlined from 'open_lib' at nmgetlib.c:390:26:
+ inlined from 'add_annot_def' at doinit.c:627:7:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
-nmgetlib.c: In function 'open_lib':
-nmgetlib.c:2267:12: note: length computed here
- 2267 | fn_len = strlen(f_name);
- | ^
+doinit.c: In function 'add_annot_def':
+doinit.c:627:7: note: length computed here
+ 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1));
+ | ^
In function 'strncpy',
- inlined from 'add_file' at lib_sel.c:317:5:
+ inlined from 'add_annot_def' at doinit.c:627:7:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
-lib_sel.c: In function 'add_file':
-lib_sel.c:311:7: note: length computed here
- 311 | len=strlen(tname)+1;
+doinit.c: In function 'add_annot_def':
+doinit.c:627:7: note: length computed here
+ 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1));
+ | ^
+In function 'strncpy',
+ inlined from 'add_annot_def' at doinit.c:627:7:
+/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
+ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
+ | ^
+doinit.c: In function 'add_annot_def':
+doinit.c:627:7: note: length computed here
+ 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1));
| ^
In function 'strncpy',
inlined from 'add_file' at lib_sel.c:317:5:
@@ -2007,14 +2434,35 @@
2267 | fn_len = strlen(f_name);
| ^
In function 'strncpy',
- inlined from 'add_file' at lib_sel.c:317:5:
+ inlined from 'alloc_file_name' at nmgetlib.c:2274:5,
+ inlined from 'open_lib' at nmgetlib.c:390:26:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
-lib_sel.c: In function 'add_file':
-lib_sel.c:311:7: note: length computed here
- 311 | len=strlen(tname)+1;
- | ^
+nmgetlib.c: In function 'open_lib':
+nmgetlib.c:2267:12: note: length computed here
+ 2267 | fn_len = strlen(f_name);
+ | ^
+In function 'strncpy',
+ inlined from 'alloc_file_name' at nmgetlib.c:2274:5,
+ inlined from 'open_lib' at nmgetlib.c:390:26:
+/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
+ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
+ | ^
+nmgetlib.c: In function 'open_lib':
+nmgetlib.c:2267:12: note: length computed here
+ 2267 | fn_len = strlen(f_name);
+ | ^
+In function 'strncpy',
+ inlined from 'alloc_file_name' at nmgetlib.c:2274:5,
+ inlined from 'open_lib' at nmgetlib.c:390:26:
+/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
+ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
+ | ^
+nmgetlib.c: In function 'open_lib':
+nmgetlib.c:2267:12: note: length computed here
+ 2267 | fn_len = strlen(f_name);
+ | ^
In function 'strncpy',
inlined from 'showalign.constprop' at mshowalign2.c:577:8:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
@@ -2047,6 +2495,16 @@
2267 | fn_len = strlen(f_name);
| ^
In function 'strncpy',
+ inlined from 'alloc_file_name' at nmgetlib.c:2274:5,
+ inlined from 'open_lib' at nmgetlib.c:390:26:
+/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
+ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
+ | ^
+nmgetlib.c: In function 'open_lib':
+nmgetlib.c:2267:12: note: length computed here
+ 2267 | fn_len = strlen(f_name);
+ | ^
+In function 'strncpy',
inlined from 'showalign.constprop' at mshowalign2.c:577:8:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
@@ -2078,6 +2536,24 @@
2267 | fn_len = strlen(f_name);
| ^
In function 'strncpy',
+ inlined from 'add_file' at lib_sel.c:317:5:
+/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
+ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
+ | ^
+lib_sel.c: In function 'add_file':
+lib_sel.c:311:7: note: length computed here
+ 311 | len=strlen(tname)+1;
+ | ^
+In function 'strncpy',
+ inlined from 'add_file' at lib_sel.c:317:5:
+/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
+ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
+ | ^
+lib_sel.c: In function 'add_file':
+lib_sel.c:311:7: note: length computed here
+ 311 | len=strlen(tname)+1;
+ | ^
+In function 'strncpy',
inlined from 'alloc_file_name' at nmgetlib.c:2274:5,
inlined from 'open_lib' at nmgetlib.c:390:26:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
@@ -2098,26 +2574,34 @@
2267 | fn_len = strlen(f_name);
| ^
In function 'strncpy',
- inlined from 'showalign.constprop' at mshowalign2.c:577:8:
+ inlined from 'alloc_file_name' at nmgetlib.c:2274:5,
+ inlined from 'open_lib' at nmgetlib.c:390:26:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
-mshowalign2.c: In function 'showalign.constprop':
-mshowalign2.c:577:8: note: length computed here
- 577 | SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string));
- | ^
+nmgetlib.c: In function 'open_lib':
+nmgetlib.c:2267:12: note: length computed here
+ 2267 | fn_len = strlen(f_name);
+ | ^
In function 'strncpy',
- inlined from 'encode_json_lines' at url_subs.c:68:3,
- inlined from 'do_url1' at url_subs.c:307:42,
- inlined from 'do_show' at mshowalign2.c:864:7,
- inlined from 'showalign.constprop' at mshowalign2.c:761:7:
+ inlined from 'alloc_file_name' at nmgetlib.c:2274:5,
+ inlined from 'open_lib' at nmgetlib.c:390:26:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
-mshowalign2.c: In function 'showalign.constprop':
-url_subs.c:61:19: note: length computed here
- 61 | n_tmp_annot_s = strlen(annot_s)+1;
- | ^
+nmgetlib.c: In function 'open_lib':
+nmgetlib.c:2267:12: note: length computed here
+ 2267 | fn_len = strlen(f_name);
+ | ^
+In function 'strncpy',
+ inlined from 'add_file' at lib_sel.c:317:5:
+/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
+ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
+ | ^
+lib_sel.c: In function 'add_file':
+lib_sel.c:311:7: note: length computed here
+ 311 | len=strlen(tname)+1;
+ | ^
In function 'strncpy',
inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
@@ -2137,6 +2621,16 @@
311 | len=strlen(tname)+1;
| ^
In function 'strncpy',
+ inlined from 'alloc_file_name' at nmgetlib.c:2274:5,
+ inlined from 'open_lib' at nmgetlib.c:390:26:
+/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
+ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
+ | ^
+nmgetlib.c: In function 'open_lib':
+nmgetlib.c:2267:12: note: length computed here
+ 2267 | fn_len = strlen(f_name);
+ | ^
+In function 'strncpy',
inlined from 'add_file' at lib_sel.c:317:5:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
@@ -2146,6 +2640,27 @@
311 | len=strlen(tname)+1;
| ^
In function 'strncpy',
+ inlined from 'showalign.constprop' at mshowalign2.c:577:8:
+/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
+ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
+ | ^
+mshowalign2.c: In function 'showalign.constprop':
+mshowalign2.c:577:8: note: length computed here
+ 577 | SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string));
+ | ^
+In function 'strncpy',
+ inlined from 'encode_json_lines' at url_subs.c:68:3,
+ inlined from 'do_url1' at url_subs.c:307:42,
+ inlined from 'do_show' at mshowalign2.c:864:7,
+ inlined from 'showalign.constprop' at mshowalign2.c:761:7:
+/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
+ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
+ | ^
+mshowalign2.c: In function 'showalign.constprop':
+url_subs.c:61:19: note: length computed here
+ 61 | n_tmp_annot_s = strlen(annot_s)+1;
+ | ^
+In function 'strncpy',
inlined from 'add_file' at lib_sel.c:317:5:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
@@ -2155,6 +2670,15 @@
311 | len=strlen(tname)+1;
| ^
In function 'strncpy',
+ inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2:
+/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
+ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
+ | ^
+compacc2e.c: In function 'next_annot_entry.constprop':
+compacc2e.c:2035:2: note: length computed here
+ 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment));
+ | ^
+In function 'strncpy',
inlined from 'add_file' at lib_sel.c:317:5:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
@@ -2181,6 +2705,13 @@
lib_sel.c:311:7: note: length computed here
311 | len=strlen(tname)+1;
| ^
+initfa.c: In function 'get_lambda.constprop':
+initfa.c:2224:24: warning: argument 1 value '2294967297' exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
+ 2224 | if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) {
+ | ^
+/usr/include/stdlib.h:542:14: note: in a call to allocation function 'calloc' declared here
+ 542 | extern void *calloc (size_t __nmemb, size_t __size)
+ | ^
In function 'strncpy',
inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
@@ -2200,32 +2731,23 @@
2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment));
| ^
In function 'strncpy',
- inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2:
-/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
- 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
- | ^
-compacc2e.c: In function 'next_annot_entry.constprop':
-compacc2e.c:2035:2: note: length computed here
- 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment));
- | ^
-In function 'strncpy',
- inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2:
+ inlined from 'add_file' at lib_sel.c:317:5:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
-compacc2e.c: In function 'next_annot_entry.constprop':
-compacc2e.c:2035:2: note: length computed here
- 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment));
- | ^
+lib_sel.c: In function 'add_file':
+lib_sel.c:311:7: note: length computed here
+ 311 | len=strlen(tname)+1;
+ | ^
In function 'strncpy',
- inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2:
+ inlined from 'add_file' at lib_sel.c:317:5:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
-compacc2e.c: In function 'next_annot_entry.constprop':
-compacc2e.c:2035:2: note: length computed here
- 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment));
- | ^
+lib_sel.c: In function 'add_file':
+lib_sel.c:311:7: note: length computed here
+ 311 | len=strlen(tname)+1;
+ | ^
In function 'strncpy',
inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
@@ -2257,6 +2779,15 @@
61 | n_tmp_annot_s = strlen(annot_s)+1;
| ^
In function 'strncpy',
+ inlined from 'add_file' at lib_sel.c:317:5:
+/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
+ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
+ | ^
+lib_sel.c: In function 'add_file':
+lib_sel.c:311:7: note: length computed here
+ 311 | len=strlen(tname)+1;
+ | ^
+In function 'strncpy',
inlined from 'showalign.constprop' at mshowalign2.c:577:8:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
@@ -2277,6 +2808,24 @@
url_subs.c:61:19: note: length computed here
61 | n_tmp_annot_s = strlen(annot_s)+1;
| ^
+In function 'strncpy',
+ inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2:
+/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
+ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
+ | ^
+compacc2e.c: In function 'next_annot_entry.constprop':
+compacc2e.c:2035:2: note: length computed here
+ 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment));
+ | ^
+In function 'strncpy',
+ inlined from 'add_file' at lib_sel.c:317:5:
+/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
+ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
+ | ^
+lib_sel.c: In function 'add_file':
+lib_sel.c:311:7: note: length computed here
+ 311 | len=strlen(tname)+1;
+ | ^
initfa.c: In function 'get_lambda.constprop':
initfa.c:2224:24: warning: argument 1 value '2294967297' exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
2224 | if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) {
@@ -2284,22 +2833,6 @@
/usr/include/stdlib.h:542:14: note: in a call to allocation function 'calloc' declared here
542 | extern void *calloc (size_t __nmemb, size_t __size)
| ^
-initfa.c: In function 'get_lambda.constprop':
-initfa.c:2224:24: warning: argument 1 value '2294967297' exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
- 2224 | if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) {
- | ^
-/usr/include/stdlib.h:542:14: note: in a call to allocation function 'calloc' declared here
- 542 | extern void *calloc (size_t __nmemb, size_t __size)
- | ^
-In function 'strncpy',
- inlined from 'build_ares_code.isra' at build_ares.c:217:4:
-/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
- 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
- | ^
-build_ares.c: In function 'build_ares_code.isra':
-build_ares.c:217:59: note: length computed here
- 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2);
- | ^
In function 'strncpy',
inlined from 'showalign.constprop' at mshowalign2.c:577:8:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
@@ -2321,91 +2854,13 @@
url_subs.c:61:19: note: length computed here
61 | n_tmp_annot_s = strlen(annot_s)+1;
| ^
-In function 'strncpy',
- inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2:
-/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
- 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
- | ^
-compacc2e.c: In function 'next_annot_entry.constprop':
-compacc2e.c:2035:2: note: length computed here
- 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment));
- | ^
-In function 'strncpy',
- inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2:
-/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
- 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
- | ^
-compacc2e.c: In function 'next_annot_entry.constprop':
-compacc2e.c:2035:2: note: length computed here
- 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment));
- | ^
-/usr/bin/ld: /tmp/fasts36.fLa5hP.ltrans0.ltrans.o: in function `.L1693':
-/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
-In function 'strncpy',
- inlined from 'build_ares_code.isra' at build_ares.c:217:4:
-/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
- 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
- | ^
-build_ares.c: In function 'build_ares_code.isra':
-build_ares.c:217:59: note: length computed here
- 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2);
- | ^
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/tfastm36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_s.o htime.o apam.o doinit.o init_tfm.o drop_tfm.o calcons_tfm.o scaleswts.o tatstats_fm.o last_tat.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o mrandom.o url_subs.o -lm -lpthread
-In function 'strncpy',
- inlined from 'build_ares_code.isra' at build_ares.c:217:4:
-/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
- 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
- | ^
-build_ares.c: In function 'build_ares_code.isra':
-build_ares.c:217:59: note: length computed here
- 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2);
- | ^
-compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch]
- 954 | re_openlib(struct lmf_str *, int outtty);
- | ^
-nmgetlib.c:503:3: note: type mismatch in parameter 2
- 503 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty)
- | ^
-nmgetlib.c:503:3: note: 're_openlib' was previously declared here
-nmgetlib.c:503:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used
-mshowbest.c:63:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch]
- 63 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr);
- | ^
-compacc2e.c:2290:1: note: type mismatch in parameter 2
- 2290 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) {
- | ^
-compacc2e.c:2290:1: note: 's_annot_to_aa1a' was previously declared here
-compacc2e.c:2290:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
-comp_lib9.c:236:1: warning: type of 'process_hist' does not match original declaration [-Wlto-type-mismatch]
- 236 | process_hist(struct stat_str *sptr, int nstats,
- | ^
-scaleswt.c:164:1: note: type mismatch in parameter 7
- 164 | process_hist(struct stat_str *sptr, int nstats,
- | ^
-scaleswt.c:164:1: note: 'process_hist' was previously declared here
-scaleswt.c:164:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
-mshowbest.c:82:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch]
- 82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p,
- | ^
-compacc2e.c:2178:1: note: type mismatch in parameter 5
- 2178 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, long offset, int n1, struct annot_str **annot_p,
- | ^
-compacc2e.c:2178:1: note: 'get_annot' was previously declared here
-compacc2e.c:2178:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
-mshowalign2.c:85:1: warning: type of 'buf_align_seq' does not match original declaration [-Wlto-type-mismatch]
- 85 | buf_align_seq(unsigned char **aa0, int n0,
- | ^
-compacc2e.c:3575:1: note: type mismatch in parameter 8
- 3575 | buf_align_seq(unsigned char **aa0, int n0,
- | ^
-compacc2e.c:3575:1: note: 'buf_align_seq' was previously declared here
-comp_lib9.c:287:1: warning: type of 'showalign' does not match original declaration [-Wlto-type-mismatch]
- 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn,
- | ^
-mshowalign2.c:134:6: note: 'showalign' was previously declared here
- 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn,
- | ^
-mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used
+initfa.c: In function 'get_lambda.constprop':
+initfa.c:2224:24: warning: argument 1 value '2294967297' exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
+ 2224 | if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) {
+ | ^
+/usr/include/stdlib.h:542:14: note: in a call to allocation function 'calloc' declared here
+ 542 | extern void *calloc (size_t __nmemb, size_t __size)
+ | ^
In function 'strncpy',
inlined from 'showalign.constprop' at mshowalign2.c:577:8:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
@@ -2428,6 +2883,15 @@
61 | n_tmp_annot_s = strlen(annot_s)+1;
| ^
In function 'strncpy',
+ inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2:
+/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
+ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
+ | ^
+compacc2e.c: In function 'next_annot_entry.constprop':
+compacc2e.c:2035:2: note: length computed here
+ 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment));
+ | ^
+In function 'strncpy',
inlined from 'showalign.constprop.isra' at mshowalign2.c:577:8:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
@@ -2448,96 +2912,12 @@
url_subs.c:61:19: note: length computed here
61 | n_tmp_annot_s = strlen(annot_s)+1;
| ^
-/usr/bin/ld: /tmp/fastm36.Xklut8.ltrans0.ltrans.o: in function `.L1693':
-/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
-/usr/bin/ld: /tmp/tfasts36.mUpTxw.ltrans0.ltrans.o: in function `.L1845':
-/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/fastf36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_ff.o drop_ff2.o calcons_ff.o scaleswtf.o last_tat.o tatstats_ff.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o mrandom.o url_subs.o -lm -lpthread
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/tfastf36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tf.o drop_tff.o calcons_tff.o scaleswtf.o last_tat.o tatstats_ff.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o mrandom.o url_subs.o -lm -lpthread
-compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch]
- 954 | re_openlib(struct lmf_str *, int outtty);
- | ^
-nmgetlib.c:503:3: note: type mismatch in parameter 2
- 503 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty)
- | ^
-nmgetlib.c:503:3: note: 're_openlib' was previously declared here
-nmgetlib.c:503:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used
-mshowbest.c:63:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch]
- 63 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr);
- | ^
-compacc2e.c:2290:1: note: type mismatch in parameter 2
- 2290 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) {
- | ^
-compacc2e.c:2290:1: note: 's_annot_to_aa1a' was previously declared here
-compacc2e.c:2290:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
-comp_lib9.c:236:1: warning: type of 'process_hist' does not match original declaration [-Wlto-type-mismatch]
- 236 | process_hist(struct stat_str *sptr, int nstats,
- | ^
-scaleswt.c:164:1: note: type mismatch in parameter 7
- 164 | process_hist(struct stat_str *sptr, int nstats,
- | ^
-scaleswt.c:164:1: note: 'process_hist' was previously declared here
-scaleswt.c:164:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
-mshowbest.c:82:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch]
- 82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p,
- | ^
-compacc2e.c:2178:1: note: type mismatch in parameter 5
- 2178 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, long offset, int n1, struct annot_str **annot_p,
- | ^
-compacc2e.c:2178:1: note: 'get_annot' was previously declared here
-compacc2e.c:2178:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
-comp_lib9.c:287:1: warning: type of 'showalign' does not match original declaration [-Wlto-type-mismatch]
- 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn,
- | ^
-mshowalign2.c:134:6: note: 'showalign' was previously declared here
- 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn,
- | ^
-mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used
-compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch]
- 954 | re_openlib(struct lmf_str *, int outtty);
- | ^
-nmgetlib.c:503:3: note: type mismatch in parameter 2
- 503 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty)
- | ^
-nmgetlib.c:503:3: note: 're_openlib' was previously declared here
-nmgetlib.c:503:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used
-mshowbest.c:63:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch]
- 63 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr);
- | ^
-compacc2e.c:2290:1: note: type mismatch in parameter 2
- 2290 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) {
- | ^
-compacc2e.c:2290:1: note: 's_annot_to_aa1a' was previously declared here
-compacc2e.c:2290:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
-comp_lib9.c:236:1: warning: type of 'process_hist' does not match original declaration [-Wlto-type-mismatch]
- 236 | process_hist(struct stat_str *sptr, int nstats,
- | ^
-scaleswt.c:164:1: note: type mismatch in parameter 7
- 164 | process_hist(struct stat_str *sptr, int nstats,
- | ^
-scaleswt.c:164:1: note: 'process_hist' was previously declared here
-scaleswt.c:164:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
-mshowbest.c:82:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch]
- 82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p,
- | ^
-compacc2e.c:2178:1: note: type mismatch in parameter 5
- 2178 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, long offset, int n1, struct annot_str **annot_p,
- | ^
-compacc2e.c:2178:1: note: 'get_annot' was previously declared here
-compacc2e.c:2178:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
-comp_lib9.c:287:1: warning: type of 'showalign' does not match original declaration [-Wlto-type-mismatch]
- 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn,
- | ^
-mshowalign2.c:134:6: note: 'showalign' was previously declared here
- 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn,
- | ^
-mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used
In function 'strncpy',
- inlined from 'showalign.constprop.isra' at mshowalign2.c:577:8:
+ inlined from 'showalign.constprop' at mshowalign2.c:577:8:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
-mshowalign2.c: In function 'showalign.constprop.isra':
+mshowalign2.c: In function 'showalign.constprop':
mshowalign2.c:577:8: note: length computed here
577 | SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string));
| ^
@@ -2545,11 +2925,11 @@
inlined from 'encode_json_lines' at url_subs.c:68:3,
inlined from 'do_url1' at url_subs.c:307:42,
inlined from 'do_show' at mshowalign2.c:864:7,
- inlined from 'showalign.constprop.isra' at mshowalign2.c:761:7:
+ inlined from 'showalign.constprop' at mshowalign2.c:761:7:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
-mshowalign2.c: In function 'showalign.constprop.isra':
+mshowalign2.c: In function 'showalign.constprop':
url_subs.c:61:19: note: length computed here
61 | n_tmp_annot_s = strlen(annot_s)+1;
| ^
@@ -2563,154 +2943,6 @@
217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2);
| ^
In function 'strncpy',
- inlined from 'build_ares_code.isra' at build_ares.c:217:4:
-/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
- 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
- | ^
-build_ares.c: In function 'build_ares_code.isra':
-build_ares.c:217:59: note: length computed here
- 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2);
- | ^
-In function 'strncpy',
- inlined from 'add_annot_def' at doinit.c:627:7:
-/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
- 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
- | ^
-doinit.c: In function 'add_annot_def':
-doinit.c:627:7: note: length computed here
- 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1));
- | ^
-/usr/bin/ld: /tmp/fasty36.33ziFV.ltrans0.ltrans.o: in function `.L1722':
-/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/glsearch36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_lnw_sse.o droplnw_sse.o glocal_sse2.o gwm_align.o calcons_sw.o scale_sn.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lpthread
-In function 'strncpy',
- inlined from 'set_opt_disp_defs' at doinit.c:991:4,
- inlined from 'f_init_opts' at initfa.c:476:3,
- inlined from 'f_initenv' at initfa.c:985:3,
- inlined from 'initenv' at doinit.c:359:4,
- inlined from 'main' at comp_lib9.c:576:3:
-/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
- 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
- | ^
-comp_lib9.c: In function 'main':
-doinit.c:991:4: note: length computed here
- 991 | strncpy(this_opt->s_param,s_param,strlen(s_param));
- | ^
-In function 'strncpy',
- inlined from 'pre_parse_markx' at doinit.c:785:5,
- inlined from 'initenv' at doinit.c:402:4,
- inlined from 'main' at comp_lib9.c:576:3:
-/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
- 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
- | ^
-comp_lib9.c: In function 'main':
-doinit.c:785:5: note: length computed here
- 785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1));
- | ^
-compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch]
- 954 | re_openlib(struct lmf_str *, int outtty);
- | ^
-nmgetlib.c:503:3: note: type mismatch in parameter 2
- 503 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty)
- | ^
-nmgetlib.c:503:3: note: 're_openlib' was previously declared here
-nmgetlib.c:503:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used
-mshowbest.c:63:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch]
- 63 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr);
- | ^
-compacc2e.c:2290:1: note: type mismatch in parameter 2
- 2290 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) {
- | ^
-compacc2e.c:2290:1: note: 's_annot_to_aa1a' was previously declared here
-compacc2e.c:2290:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
-comp_lib9.c:250:5: warning: type of 'last_calc' does not match original declaration [-Wlto-type-mismatch]
- 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn,
- | ^
-initfa.c:2036:1: note: type mismatch in parameter 6
- 2036 | last_calc(
- | ^
-initfa.c:2036:1: note: 'last_calc' was previously declared here
-mshowbest.c:82:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch]
- 82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p,
- | ^
-compacc2e.c:2178:1: note: type mismatch in parameter 5
- 2178 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, long offset, int n1, struct annot_str **annot_p,
- | ^
-compacc2e.c:2178:1: note: 'get_annot' was previously declared here
-compacc2e.c:2178:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
-comp_lib9.c:287:1: warning: type of 'showalign' does not match original declaration [-Wlto-type-mismatch]
- 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn,
- | ^
-mshowalign2.c:134:6: note: 'showalign' was previously declared here
- 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn,
- | ^
-mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used
-/usr/bin/ld: /tmp/fastx36.q4Cuy8.ltrans0.ltrans.o: in function `.L1729':
-/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
-/usr/bin/ld: /tmp/tfastx36.r9wla5.ltrans0.ltrans.o: in function `.L1662':
-/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
-cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/ggsearch36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_gnw_sse.o dropgnw_sse.o global_sse2.o gwm_align.o calcons_sw.o scale_sn.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lpthread
-In function 'strncpy',
- inlined from 'add_annot_def' at doinit.c:627:7:
-/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
- 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
- | ^
-doinit.c: In function 'add_annot_def':
-doinit.c:627:7: note: length computed here
- 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1));
- | ^
-compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch]
- 954 | re_openlib(struct lmf_str *, int outtty);
- | ^
-nmgetlib.c:503:3: note: type mismatch in parameter 2
- 503 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty)
- | ^
-nmgetlib.c:503:3: note: 're_openlib' was previously declared here
-nmgetlib.c:503:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used
-mshowbest.c:63:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch]
- 63 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr);
- | ^
-compacc2e.c:2290:1: note: type mismatch in parameter 2
- 2290 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) {
- | ^
-compacc2e.c:2290:1: note: 's_annot_to_aa1a' was previously declared here
-compacc2e.c:2290:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
-comp_lib9.c:250:5: warning: type of 'last_calc' does not match original declaration [-Wlto-type-mismatch]
- 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn,
- | ^
-initfa.c:2036:1: note: type mismatch in parameter 6
- 2036 | last_calc(
- | ^
-initfa.c:2036:1: note: 'last_calc' was previously declared here
-mshowbest.c:82:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch]
- 82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p,
- | ^
-compacc2e.c:2178:1: note: type mismatch in parameter 5
- 2178 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, long offset, int n1, struct annot_str **annot_p,
- | ^
-compacc2e.c:2178:1: note: 'get_annot' was previously declared here
-compacc2e.c:2178:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
-comp_lib9.c:287:1: warning: type of 'showalign' does not match original declaration [-Wlto-type-mismatch]
- 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn,
- | ^
-mshowalign2.c:134:6: note: 'showalign' was previously declared here
- 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn,
- | ^
-mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used
-In function 'strncpy',
- inlined from 'add_annot_def' at doinit.c:627:7:
-/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
- 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
- | ^
-doinit.c: In function 'add_annot_def':
-doinit.c:627:7: note: length computed here
- 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1));
- | ^
-/usr/bin/ld: /tmp/tfasty36.TrXS1I.ltrans0.ltrans.o: in function `.L1729':
-/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
-/usr/bin/ld: /tmp/fasta36.VCOpl2.ltrans0.ltrans.o: in function `.L1641':
-/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
-In function 'strncpy',
inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
@@ -2720,35 +2952,11 @@
2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment));
| ^
In function 'strncpy',
- inlined from 'set_opt_disp_defs' at doinit.c:991:4,
- inlined from 'f_init_opts' at initfa.c:476:3,
- inlined from 'f_initenv' at initfa.c:985:3,
- inlined from 'initenv' at doinit.c:359:4,
- inlined from 'main' at comp_lib9.c:576:3:
-/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
- 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
- | ^
-comp_lib9.c: In function 'main':
-doinit.c:991:4: note: length computed here
- 991 | strncpy(this_opt->s_param,s_param,strlen(s_param));
- | ^
-In function 'strncpy',
- inlined from 'pre_parse_markx' at doinit.c:785:5,
- inlined from 'initenv' at doinit.c:402:4,
- inlined from 'main' at comp_lib9.c:576:3:
-/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
- 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
- | ^
-comp_lib9.c: In function 'main':
-doinit.c:785:5: note: length computed here
- 785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1));
- | ^
-In function 'strncpy',
- inlined from 'showalign.constprop.isra' at mshowalign2.c:577:8:
+ inlined from 'showalign.constprop' at mshowalign2.c:577:8:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
-mshowalign2.c: In function 'showalign.constprop.isra':
+mshowalign2.c: In function 'showalign.constprop':
mshowalign2.c:577:8: note: length computed here
577 | SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string));
| ^
@@ -2756,82 +2964,44 @@
inlined from 'encode_json_lines' at url_subs.c:68:3,
inlined from 'do_url1' at url_subs.c:307:42,
inlined from 'do_show' at mshowalign2.c:864:7,
- inlined from 'showalign.constprop.isra' at mshowalign2.c:761:7:
+ inlined from 'showalign.constprop' at mshowalign2.c:761:7:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
-mshowalign2.c: In function 'showalign.constprop.isra':
+mshowalign2.c: In function 'showalign.constprop':
url_subs.c:61:19: note: length computed here
61 | n_tmp_annot_s = strlen(annot_s)+1;
| ^
-In function 'strncpy',
- inlined from 'set_opt_disp_defs' at doinit.c:991:4,
- inlined from 'f_init_opts' at initfa.c:476:3,
- inlined from 'f_initenv' at initfa.c:985:3,
- inlined from 'initenv' at doinit.c:359:4,
- inlined from 'main' at comp_lib9.c:576:3:
-/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
- 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
- | ^
-comp_lib9.c: In function 'main':
-doinit.c:991:4: note: length computed here
- 991 | strncpy(this_opt->s_param,s_param,strlen(s_param));
- | ^
-In function 'strncpy',
- inlined from 'pre_parse_markx' at doinit.c:785:5,
- inlined from 'initenv' at doinit.c:402:4,
- inlined from 'main' at comp_lib9.c:576:3:
-/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
- 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
- | ^
-comp_lib9.c: In function 'main':
-doinit.c:785:5: note: length computed here
- 785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1));
- | ^
-In function 'strncpy',
- inlined from 'build_ares_code' at build_ares.c:217:4:
-/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
- 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
- | ^
-build_ares.c: In function 'build_ares_code':
-build_ares.c:217:59: note: length computed here
- 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2);
- | ^
-In function 'strncpy',
- inlined from 'build_ares_code' at build_ares.c:217:4:
-/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
- 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
- | ^
-build_ares.c: In function 'build_ares_code':
-build_ares.c:217:59: note: length computed here
- 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2);
- | ^
-/usr/bin/ld: /tmp/ssearch36.HSTTlV.ltrans0.ltrans.o: in function `.L1748':
+/usr/bin/ld: /tmp/fasts36.oupEVU.ltrans0.ltrans.o: in function `.L1693':
/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
In function 'strncpy',
- inlined from 'set_opt_disp_defs' at doinit.c:991:4,
- inlined from 'f_init_opts' at initfa.c:476:3,
- inlined from 'f_initenv' at initfa.c:985:3,
- inlined from 'initenv' at doinit.c:359:4,
- inlined from 'main' at comp_lib9.c:576:3:
+ inlined from 'showalign.constprop' at mshowalign2.c:577:8:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
-comp_lib9.c: In function 'main':
-doinit.c:991:4: note: length computed here
- 991 | strncpy(this_opt->s_param,s_param,strlen(s_param));
- | ^
+mshowalign2.c: In function 'showalign.constprop':
+mshowalign2.c:577:8: note: length computed here
+ 577 | SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string));
+ | ^
+initfa.c: In function 'get_lambda.constprop':
+initfa.c:2224:24: warning: argument 1 value '2294967297' exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
+ 2224 | if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) {
+ | ^
+/usr/include/stdlib.h:542:14: note: in a call to allocation function 'calloc' declared here
+ 542 | extern void *calloc (size_t __nmemb, size_t __size)
+ | ^
In function 'strncpy',
- inlined from 'pre_parse_markx' at doinit.c:785:5,
- inlined from 'initenv' at doinit.c:402:4,
- inlined from 'main' at comp_lib9.c:576:3:
+ inlined from 'encode_json_lines' at url_subs.c:68:3,
+ inlined from 'do_url1' at url_subs.c:307:42,
+ inlined from 'do_show' at mshowalign2.c:864:7,
+ inlined from 'showalign.constprop' at mshowalign2.c:761:7:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
-comp_lib9.c: In function 'main':
-doinit.c:785:5: note: length computed here
- 785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1));
- | ^
+mshowalign2.c: In function 'showalign.constprop':
+url_subs.c:61:19: note: length computed here
+ 61 | n_tmp_annot_s = strlen(annot_s)+1;
+ | ^
In function 'strncpy',
inlined from 'build_ares_code.isra' at build_ares.c:217:4:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
@@ -2842,112 +3012,31 @@
217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2);
| ^
In function 'strncpy',
- inlined from 'set_opt_disp_defs' at doinit.c:991:4,
- inlined from 'f_init_opts' at initfa.c:476:3,
- inlined from 'f_initenv' at initfa.c:985:3,
- inlined from 'initenv' at doinit.c:359:4,
- inlined from 'main' at comp_lib9.c:576:3:
-/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
- 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
- | ^
-comp_lib9.c: In function 'main':
-doinit.c:991:4: note: length computed here
- 991 | strncpy(this_opt->s_param,s_param,strlen(s_param));
- | ^
-In function 'strncpy',
- inlined from 'pre_parse_markx' at doinit.c:785:5,
- inlined from 'initenv' at doinit.c:402:4,
- inlined from 'main' at comp_lib9.c:576:3:
+ inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
-comp_lib9.c: In function 'main':
-doinit.c:785:5: note: length computed here
- 785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1));
- | ^
-/usr/bin/ld: /tmp/lalign36.BlICJd.ltrans0.ltrans.o: in function `.L1911':
+compacc2e.c: In function 'next_annot_entry.constprop':
+compacc2e.c:2035:2: note: length computed here
+ 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment));
+ | ^
+/usr/bin/ld: /tmp/fastm36.XpG1BR.ltrans0.ltrans.o: in function `.L1693':
/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
In function 'strncpy',
- inlined from 'alloc_file_name' at nmgetlib.c:2274:5,
- inlined from 'open_lib' at nmgetlib.c:390:26:
-/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
- 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
- | ^
-nmgetlib.c: In function 'open_lib':
-nmgetlib.c:2267:12: note: length computed here
- 2267 | fn_len = strlen(f_name);
- | ^
-In function 'strncpy',
- inlined from 'alloc_file_name' at nmgetlib.c:2274:5,
- inlined from 'open_lib' at nmgetlib.c:390:26:
-/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
- 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
- | ^
-nmgetlib.c: In function 'open_lib':
-nmgetlib.c:2267:12: note: length computed here
- 2267 | fn_len = strlen(f_name);
- | ^
-In function 'strncpy',
- inlined from 'add_annot_def' at doinit.c:627:7:
-/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
- 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
- | ^
-doinit.c: In function 'add_annot_def':
-doinit.c:627:7: note: length computed here
- 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1));
- | ^
-In function 'strncpy',
- inlined from 'add_annot_def' at doinit.c:627:7:
-/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
- 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
- | ^
-doinit.c: In function 'add_annot_def':
-doinit.c:627:7: note: length computed here
- 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1));
- | ^
-In function 'strncpy',
- inlined from 'alloc_file_name' at nmgetlib.c:2274:5,
- inlined from 'open_lib' at nmgetlib.c:390:26:
-/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
- 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
- | ^
-nmgetlib.c: In function 'open_lib':
-nmgetlib.c:2267:12: note: length computed here
- 2267 | fn_len = strlen(f_name);
- | ^
-In function 'strncpy',
- inlined from 'add_file' at lib_sel.c:317:5:
-/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
- 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
- | ^
-lib_sel.c: In function 'add_file':
-lib_sel.c:311:7: note: length computed here
- 311 | len=strlen(tname)+1;
- | ^
-In function 'strncpy',
- inlined from 'add_file' at lib_sel.c:317:5:
-/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
- 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
- | ^
-lib_sel.c: In function 'add_file':
-lib_sel.c:311:7: note: length computed here
- 311 | len=strlen(tname)+1;
- | ^
-In function 'strncpy',
- inlined from 'add_file' at lib_sel.c:317:5:
+ inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
-lib_sel.c: In function 'add_file':
-lib_sel.c:311:7: note: length computed here
- 311 | len=strlen(tname)+1;
- | ^
+compacc2e.c: In function 'next_annot_entry.constprop':
+compacc2e.c:2035:2: note: length computed here
+ 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment));
+ | ^
In function 'strncpy',
- inlined from 'showalign.constprop' at mshowalign2.c:577:8:
+ inlined from 'showalign.constprop.isra' at mshowalign2.c:577:8:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
-mshowalign2.c: In function 'showalign.constprop':
+mshowalign2.c: In function 'showalign.constprop.isra':
mshowalign2.c:577:8: note: length computed here
577 | SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string));
| ^
@@ -2955,11 +3044,11 @@
inlined from 'encode_json_lines' at url_subs.c:68:3,
inlined from 'do_url1' at url_subs.c:307:42,
inlined from 'do_show' at mshowalign2.c:864:7,
- inlined from 'showalign.constprop' at mshowalign2.c:761:7:
+ inlined from 'showalign.constprop.isra' at mshowalign2.c:761:7:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
-mshowalign2.c: In function 'showalign.constprop':
+mshowalign2.c: In function 'showalign.constprop.isra':
url_subs.c:61:19: note: length computed here
61 | n_tmp_annot_s = strlen(annot_s)+1;
| ^
@@ -2982,25 +3071,58 @@
2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment));
| ^
In function 'strncpy',
- inlined from 'alloc_file_name' at nmgetlib.c:2274:5,
- inlined from 'open_lib' at nmgetlib.c:390:26:
+ inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
-nmgetlib.c: In function 'open_lib':
-nmgetlib.c:2267:12: note: length computed here
- 2267 | fn_len = strlen(f_name);
- | ^
+compacc2e.c: In function 'next_annot_entry.constprop':
+compacc2e.c:2035:2: note: length computed here
+ 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment));
+ | ^
In function 'strncpy',
- inlined from 'alloc_file_name' at nmgetlib.c:2274:5,
- inlined from 'open_lib' at nmgetlib.c:390:26:
+ inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
-nmgetlib.c: In function 'open_lib':
-nmgetlib.c:2267:12: note: length computed here
- 2267 | fn_len = strlen(f_name);
- | ^
+compacc2e.c: In function 'next_annot_entry.constprop':
+compacc2e.c:2035:2: note: length computed here
+ 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment));
+ | ^
+In function 'strncpy',
+ inlined from 'build_ares_code.isra' at build_ares.c:217:4:
+/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
+ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
+ | ^
+build_ares.c: In function 'build_ares_code.isra':
+build_ares.c:217:59: note: length computed here
+ 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2);
+ | ^
+/usr/bin/ld: /tmp/fasta36.M5UJj2.ltrans0.ltrans.o: in function `.L1641':
+/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
+In function 'strncpy',
+ inlined from 'build_ares_code.isra' at build_ares.c:217:4:
+/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
+ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
+ | ^
+build_ares.c: In function 'build_ares_code.isra':
+build_ares.c:217:59: note: length computed here
+ 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2);
+ | ^
+In function 'strncpy',
+ inlined from 'build_ares_code.isra' at build_ares.c:217:4:
+/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
+ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
+ | ^
+build_ares.c: In function 'build_ares_code.isra':
+build_ares.c:217:59: note: length computed here
+ 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2);
+ | ^
+/usr/bin/ld: /tmp/tfastm36.b23BEh.ltrans0.ltrans.o: in function `.L1845':
+/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
+/usr/bin/ld: /usr/bin/ld: /tmp/tfasts36.mAhYYu.ltrans0.ltrans.o: in function `.L1845':
+/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
+/tmp/fastf36.vbS1aZ.ltrans0.ltrans.o: in function `.L1858':
+/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
In function 'strncpy',
inlined from 'showalign.constprop.isra' at mshowalign2.c:577:8:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
@@ -3023,6 +3145,15 @@
61 | n_tmp_annot_s = strlen(annot_s)+1;
| ^
In function 'strncpy',
+ inlined from 'build_ares_code.isra' at build_ares.c:217:4:
+/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
+ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
+ | ^
+build_ares.c: In function 'build_ares_code.isra':
+build_ares.c:217:59: note: length computed here
+ 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2);
+ | ^
+In function 'strncpy',
inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
@@ -3052,34 +3183,11 @@
url_subs.c:61:19: note: length computed here
61 | n_tmp_annot_s = strlen(annot_s)+1;
| ^
-In function 'strncpy',
- inlined from 'add_file' at lib_sel.c:317:5:
-In function 'strncpy',
- inlined from 'add_file' at lib_sel.c:317:5:
-/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
- 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
- | ^
-/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
- 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
- | ^
-lib_sel.c: In function 'add_file':
-lib_sel.c: In function 'add_file':
-lib_sel.c:311:7: note: length computed here
- 311 | len=strlen(tname)+1;
- | ^
-lib_sel.c:311:7: note: length computed here
- 311 | len=strlen(tname)+1;
- | ^
-In function 'strncpy',
- inlined from 'build_ares_code.isra' at build_ares.c:217:4:
-/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
- 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
- | ^
-build_ares.c: In function 'build_ares_code.isra':
-build_ares.c:217:59: note: length computed here
- 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2);
- | ^
-/usr/bin/ld: /tmp/tfastm36.t66GLJ.ltrans0.ltrans.o: in function `.L1845':
+/usr/bin/ld: /tmp/tfastx36.x5Y5wR.ltrans0.ltrans.o: in function `.L1662':
+/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
+/usr/bin/ld: /tmp/tfastf36.xa2AdA.ltrans0.ltrans.o: in function `.L1828':
+/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
+/usr/bin/ld: /tmp/tfasty36.jTrSwc.ltrans0.ltrans.o: in function `.L1729':
/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
In function 'strncpy',
inlined from 'build_ares_code.isra' at build_ares.c:217:4:
@@ -3099,51 +3207,12 @@
build_ares.c:217:59: note: length computed here
217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2);
| ^
-initfa.c: In function 'get_lambda.constprop':
-/usr/bin/ld: initfa.c: In function 'get_lambda.constprop':
-initfa.c:2224:24: warning: argument 1 value '2294967297' exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
- 2224 | if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) {
- | ^
-initfa.c:2224:24: warning: argument 1 value '2294967297' exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
- 2224 | if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) {
- | ^
-/usr/include/stdlib.h:542:14: note: in a call to allocation function 'calloc' declared here
- 542 | extern void *calloc (size_t __nmemb, size_t __size)
- | ^
-/usr/include/stdlib.h:542:14: note: in a call to allocation function 'calloc' declared here
- 542 | extern void *calloc (size_t __nmemb, size_t __size)
- | ^
-/tmp/tfastf36.wF09mt.ltrans0.ltrans.o: in function `.L1828':
-/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
-/usr/bin/ld: /tmp/fastf36.wzMbfD.ltrans0.ltrans.o: in function `.L1858':
-/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
In function 'strncpy',
- inlined from 'showalign.constprop' at mshowalign2.c:577:8:
-/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
- 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
- | ^
-mshowalign2.c: In function 'showalign.constprop':
-mshowalign2.c:577:8: note: length computed here
- 577 | SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string));
- | ^
-In function 'strncpy',
- inlined from 'encode_json_lines' at url_subs.c:68:3,
- inlined from 'do_url1' at url_subs.c:307:42,
- inlined from 'do_show' at mshowalign2.c:864:7,
- inlined from 'showalign.constprop' at mshowalign2.c:761:7:
-/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
- 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
- | ^
-mshowalign2.c: In function 'showalign.constprop':
-url_subs.c:61:19: note: length computed here
- 61 | n_tmp_annot_s = strlen(annot_s)+1;
- | ^
-In function 'strncpy',
- inlined from 'showalign.constprop' at mshowalign2.c:577:8:
+ inlined from 'showalign.constprop.isra' at mshowalign2.c:577:8:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
-mshowalign2.c: In function 'showalign.constprop':
+mshowalign2.c: In function 'showalign.constprop.isra':
mshowalign2.c:577:8: note: length computed here
577 | SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string));
| ^
@@ -3151,32 +3220,31 @@
inlined from 'encode_json_lines' at url_subs.c:68:3,
inlined from 'do_url1' at url_subs.c:307:42,
inlined from 'do_show' at mshowalign2.c:864:7,
- inlined from 'showalign.constprop' at mshowalign2.c:761:7:
+ inlined from 'showalign.constprop.isra' at mshowalign2.c:761:7:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
-mshowalign2.c: In function 'showalign.constprop':
+mshowalign2.c: In function 'showalign.constprop.isra':
url_subs.c:61:19: note: length computed here
61 | n_tmp_annot_s = strlen(annot_s)+1;
| ^
+/usr/bin/ld: /tmp/ssearch36.AHVdhp.ltrans0.ltrans.o: in function `.L1748':
+/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
+/usr/bin/ld: /tmp/fastx36.vJg18W.ltrans0.ltrans.o: in function `.L1729':
+/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
+/usr/bin/ld: /tmp/fasty36.f1NGPs.ltrans0.ltrans.o: in function `.L1722':
+/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
In function 'strncpy',
- inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2:
-/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
- 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
- | ^
-compacc2e.c: In function 'next_annot_entry.constprop':
-compacc2e.c:2035:2: note: length computed here
- 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment));
- | ^
-In function 'strncpy',
- inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2:
+ inlined from 'build_ares_code.isra' at build_ares.c:217:4:
/usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
-compacc2e.c: In function 'next_annot_entry.constprop':
-compacc2e.c:2035:2: note: length computed here
- 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment));
- | ^
+build_ares.c: In function 'build_ares_code.isra':
+build_ares.c:217:59: note: length computed here
+ 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2);
+ | ^
+/usr/bin/ld: /tmp/lalign36.JOcNrq.ltrans0.ltrans.o: in function `.L1911':
+/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
global_sse2.c: In function 'max_epu16':
global_sse2.c:173:10: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi]
173 | vF = max_epu16 (vF, vTemp);
@@ -3185,9 +3253,9 @@
glocal_sse2.c:185:10: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi]
185 | vF = max_epu16 (vF, vTemp);
| ^
-/usr/bin/ld: /tmp/ggsearch36.HmG7OO.ltrans0.ltrans.o: in function `.L1725':
+/usr/bin/ld: /tmp/ggsearch36.ZHzvpr.ltrans0.ltrans.o: in function `.L1725':
/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
-/usr/bin/ld: /tmp/glsearch36.OKlyF1.ltrans0.ltrans.o: in function `.L1725':
+/usr/bin/ld: /tmp/glsearch36.iss8m1.ltrans0.ltrans.o: in function `.L1725':
/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
make[2]: Leaving directory '/build/fasta3-36.3.8h.2020-02-11/src'
# convoluted, but necessary to allow cross builds
@@ -3196,21 +3264,21 @@
make[1]: Entering directory '/build/fasta3-36.3.8h.2020-02-11'
cd test ; ./test2G.sh && ./test.sh && ../bin/fasta36 -q ../seq/mgstm1.aa ../seq/prot_test.lseg
-STARTING FASTA36 Sun Jul 4 14:55:16 -12 2021 on ionos2-i386
-Linux ionos2-i386 4.19.0-17-686-pae #1 SMP Debian 4.19.194-2 (2021-06-21) i686 GNU/Linux
+STARTING FASTA36 Sun Aug 7 23:24:54 +14 2022 on i-capture-the-hostname
+Linux i-capture-the-hostname 4.19.0-17-amd64 #1 SMP Debian 4.19.194-2 (2021-06-21) x86_64 GNU/Linux
-starting prss36(ssearch/fastx) Sun Jul 4 14:55:16 -12 2021
+starting prss36(ssearch/fastx) Sun Aug 7 23:24:54 +14 2022
done
-starting lalign36 Sun Jul 4 14:55:16 -12 2021
-FINISHED Sun Jul 4 14:57:57 -12 2021
+starting lalign36 Sun Aug 7 23:24:54 +14 2022
+FINISHED Sun Aug 7 23:26:37 +14 2022
-STARTING FASTA36 Sun Jul 4 14:57:57 -12 2021 on ionos2-i386
-Linux ionos2-i386 4.19.0-17-686-pae #1 SMP Debian 4.19.194-2 (2021-06-21) i686 GNU/Linux
+STARTING FASTA36 Sun Aug 7 23:26:37 +14 2022 on i-capture-the-hostname
+Linux i-capture-the-hostname 4.19.0-17-amd64 #1 SMP Debian 4.19.194-2 (2021-06-21) x86_64 GNU/Linux
-starting prss36(ssearch/fastx) Sun Jul 4 14:57:57 -12 2021
+starting prss36(ssearch/fastx) Sun Aug 7 23:26:37 +14 2022
done
-starting lalign36 Sun Jul 4 14:57:57 -12 2021
-FINISHED Sun Jul 4 15:00:34 -12 2021
+starting lalign36 Sun Aug 7 23:26:38 +14 2022
+FINISHED Sun Aug 7 23:28:29 +14 2022
# ../bin/fasta36 -q ../seq/mgstm1.aa ../seq/prot_test.lseg
FASTA searches a protein or DNA sequence data bank
version 36.3.8h Aug, 2019
@@ -3222,29 +3290,29 @@
Library: ../seq/prot_test.lseg
2267 residues in 12 sequences
-Statistics: (shuffled [447]) MLE statistics: Lambda= 0.1696; K=0.005856
- statistics sampled from 4 (4) to 446 sequences
+Statistics: (shuffled [417]) MLE statistics: Lambda= 0.1513; K=0.00352
+ statistics sampled from 4 (4) to 417 sequences
Algorithm: FASTA (3.8 Nov 2011) [optimized]
Parameters: BL50 matrix (15:-5), open/ext: -10/-2
ktup: 2, E-join: 1 (0.667), E-opt: 0.2 (0.333), width: 16
- Scan time: 0.020
+ Scan time: 0.000
The best scores are: opt bits E(12)
-sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu ( 218) 1242 313.4 2.6e-89
-sp|P00502|GSTA1_RAT Glutathione S-transferase alph ( 222) 237 67.5 2.8e-15
-sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Ho ( 142) 51 22.0 0.091
-sp|P00517|KAPCA_BOVIN cAMP-dependent protein kinas ( 351) 43 20.0 0.84
-sp|P14960|RBS_GUITH Ribulose bisphosphate carboxyl ( 139) 36 18.3 1.1
-sp|P01593|KV101_HUMAN Ig kappa chain V-I region AG ( 108) 31 17.1 1.9
-sp|P99998|CYC_PANTR Cytochrome c OS=Pan troglodyte ( 105) 30 16.8 2.2
-sp|P02585|TNNC2_HUMAN Troponin C, skeletal muscle ( 160) 30 16.8 3.1
-sp|P03435|HEMA_I75A3 Hemagglutinin OS=Influenza A ( 567) 37 18.5 3.3
-sp|P60615|NXL1A_BUNMU Alpha-bungarotoxin isoform A ( 95) 26 15.8 3.6
-sp|P00193|FER_PEPAS Ferredoxin OS=Peptostreptococc ( 54) 22 14.9 3.9
-sp|P01834|IGKC_HUMAN Ig kappa chain C region OS=Ho ( 106) 23 15.1 5.8
+sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu ( 218) 1242 281.0 1.5e-79
+sp|P00502|GSTA1_RAT Glutathione S-transferase alph ( 222) 237 61.6 1.6e-13
+sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Ho ( 142) 51 21.0 0.17
+sp|P00517|KAPCA_BOVIN cAMP-dependent protein kinas ( 351) 43 19.3 1.3
+sp|P14960|RBS_GUITH Ribulose bisphosphate carboxyl ( 139) 36 17.8 1.5
+sp|P01593|KV101_HUMAN Ig kappa chain V-I region AG ( 108) 31 16.7 2.4
+sp|P99998|CYC_PANTR Cytochrome c OS=Pan troglodyte ( 105) 30 16.5 2.7
+sp|P02585|TNNC2_HUMAN Troponin C, skeletal muscle ( 160) 30 16.5 3.8
+sp|P60615|NXL1A_BUNMU Alpha-bungarotoxin isoform A ( 95) 26 15.6 4.1
+sp|P00193|FER_PEPAS Ferredoxin OS=Peptostreptococc ( 54) 22 14.7 4.2
+sp|P03435|HEMA_I75A3 Hemagglutinin OS=Influenza A ( 567) 37 18.0 4.5
+sp|P01834|IGKC_HUMAN Ig kappa chain C region OS=Ho ( 106) 23 14.9 6.3
>>sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu 1 O (218 aa)
- initn: 1242 init1: 1242 opt: 1242 Z-score: 1655.3 bits: 313.4 E(12): 2.6e-89
+ initn: 1242 init1: 1242 opt: 1242 Z-score: 1480.0 bits: 281.0 E(12): 1.5e-79
Smith-Waterman score: 1242; 78.0% identity (95.4% similar) in 218 aa overlap (1-218:1-218)
10 20 30 40 50 60
@@ -3272,7 +3340,7 @@
190 200 210
>>sp|P00502|GSTA1_RAT Glutathione S-transferase alpha-1 (222 aa)
- initn: 204 init1: 73 opt: 237 Z-score: 326.0 bits: 67.5 E(12): 2.8e-15
+ initn: 204 init1: 73 opt: 237 Z-score: 294.5 bits: 61.6 E(12): 1.6e-13
Smith-Waterman score: 237; 27.4% identity (57.0% similar) in 223 aa overlap (4-218:6-218)
10 20 30 40 50
@@ -3300,7 +3368,7 @@
180 190 200 210 220
>>sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Homo s (142 aa)
- initn: 40 init1: 40 opt: 51 Z-score: 83.5 bits: 22.0 E(12): 0.091
+ initn: 40 init1: 40 opt: 51 Z-score: 78.6 bits: 21.0 E(12): 0.17
Smith-Waterman score: 51; 25.6% identity (69.2% similar) in 39 aa overlap (177-214:36-73)
150 160 170 180 190 200
@@ -3316,7 +3384,7 @@
70 80 90 100 110 120
>>sp|P00517|KAPCA_BOVIN cAMP-dependent protein kinase ca (351 aa)
- initn: 43 init1: 43 opt: 43 Z-score: 65.9 bits: 20.0 E(12): 0.84
+ initn: 43 init1: 43 opt: 43 Z-score: 62.1 bits: 19.3 E(12): 1.3
Smith-Waterman score: 54; 23.6% identity (47.2% similar) in 72 aa overlap (137-206:229-300)
110 120 130 140 150 160
@@ -3335,7 +3403,7 @@
320 330 340 350
>>sp|P14960|RBS_GUITH Ribulose bisphosphate carboxylase (139 aa)
- initn: 56 init1: 36 opt: 36 Z-score: 63.9 bits: 18.3 E(12): 1.1
+ initn: 56 init1: 36 opt: 36 Z-score: 61.1 bits: 17.8 E(12): 1.5
Smith-Waterman score: 36; 57.1% identity (85.7% similar) in 7 aa overlap (7-13:47-53)
10 20 30
@@ -3351,7 +3419,7 @@
80 90 100 110 120 130
>>sp|P01593|KV101_HUMAN Ig kappa chain V-I region AG OS= (108 aa)
- initn: 31 init1: 31 opt: 31 Z-score: 59.2 bits: 17.1 E(12): 1.9
+ initn: 31 init1: 31 opt: 31 Z-score: 57.2 bits: 16.7 E(12): 2.4
Smith-Waterman score: 33; 36.0% identity (54.0% similar) in 50 aa overlap (150-190:16-64)
120 130 140 150 160 170
@@ -3367,7 +3435,7 @@
50 60 70 80 90 100
>>sp|P99998|CYC_PANTR Cytochrome c OS=Pan troglodytes GN (105 aa)
- initn: 30 init1: 30 opt: 30 Z-score: 58.1 bits: 16.8 E(12): 2.2
+ initn: 30 init1: 30 opt: 30 Z-score: 56.2 bits: 16.5 E(12): 2.7
Smith-Waterman score: 36; 26.5% identity (54.4% similar) in 68 aa overlap (129-193:28-88)
100 110 120 130 140 150
@@ -3386,7 +3454,7 @@
sp|P10 SNK
>>sp|P02585|TNNC2_HUMAN Troponin C, skeletal muscle OS=H (160 aa)
- initn: 30 init1: 30 opt: 30 Z-score: 54.8 bits: 16.8 E(12): 3.1
+ initn: 30 init1: 30 opt: 30 Z-score: 52.9 bits: 16.5 E(12): 3.8
Smith-Waterman score: 41; 25.9% identity (63.0% similar) in 54 aa overlap (44-92:13-62)
20 30 40 50 60 70
@@ -3401,24 +3469,8 @@
sp|P02 ELGTVMRMLGQTPTKEELDAIIEEVDEDGSGTIDFEEFLVMMVRQMKEDAKGKSEEELAE
40 50 60 70 80 90
->>sp|P03435|HEMA_I75A3 Hemagglutinin OS=Influenza A viru (567 aa)
- initn: 37 init1: 37 opt: 37 Z-score: 54.2 bits: 18.5 E(12): 3.3
-Smith-Waterman score: 50; 28.2% identity (64.1% similar) in 39 aa overlap (74-111:399-437)
-
- 50 60 70 80 90 100
-sp|P10 SQWLNEKFKLGLDFPNLPYLIDGSHKITQSNAILRYLARK-HHLDGETEEERIRADIVEN
- : ... .: :... : : . : . .:.
-sp|P03 GFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEK
- 370 380 390 400 410 420
-
- 110 120 130 140 150 160
-sp|P10 QVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAGDKVTYVDFLAYD
- : ::...:
-sp|P03 YVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTRRQLRENAEDMGNGCFKIYH
- 430 440 450 460 470 480
-
>>sp|P60615|NXL1A_BUNMU Alpha-bungarotoxin isoform A31 O (95 aa)
- initn: 26 init1: 26 opt: 26 Z-score: 53.6 bits: 15.8 E(12): 3.6
+ initn: 26 init1: 26 opt: 26 Z-score: 52.3 bits: 15.6 E(12): 4.1
Smith-Waterman score: 30; 54.5% identity (63.6% similar) in 11 aa overlap (115-125:86-94)
90 100 110 120 130 140
@@ -3431,7 +3483,7 @@
sp|P10 RPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRYI
>>sp|P00193|FER_PEPAS Ferredoxin OS=Peptostreptococcus a (54 aa)
- initn: 22 init1: 22 opt: 22 Z-score: 52.7 bits: 14.9 E(12): 3.9
+ initn: 22 init1: 22 opt: 22 Z-score: 52.0 bits: 14.7 E(12): 4.2
Smith-Waterman score: 25; 50.0% identity (100.0% similar) in 4 aa overlap (171-174:15-18)
150 160 170 180 190 200
@@ -3446,8 +3498,24 @@
sp|P00 CPVGAPNPED
50
+>>sp|P03435|HEMA_I75A3 Hemagglutinin OS=Influenza A viru (567 aa)
+ initn: 37 init1: 37 opt: 37 Z-score: 51.3 bits: 18.0 E(12): 4.5
+Smith-Waterman score: 50; 28.2% identity (64.1% similar) in 39 aa overlap (74-111:399-437)
+
+ 50 60 70 80 90 100
+sp|P10 SQWLNEKFKLGLDFPNLPYLIDGSHKITQSNAILRYLARK-HHLDGETEEERIRADIVEN
+ : ... .: :... : : . : . .:.
+sp|P03 GFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEK
+ 370 380 390 400 410 420
+
+ 110 120 130 140 150 160
+sp|P10 QVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAGDKVTYVDFLAYD
+ : ::...:
+sp|P03 YVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTRRQLRENAEDMGNGCFKIYH
+ 430 440 450 460 470 480
+
>>sp|P01834|IGKC_HUMAN Ig kappa chain C region OS=Homo s (106 aa)
- initn: 23 init1: 23 opt: 23 Z-score: 48.8 bits: 15.1 E(12): 5.8
+ initn: 23 init1: 23 opt: 23 Z-score: 47.9 bits: 14.9 E(12): 6.3
Smith-Waterman score: 35; 18.3% identity (53.5% similar) in 71 aa overlap (58-124:12-82)
30 40 50 60 70 80
@@ -3472,9 +3540,9 @@
218 residues in 1 query sequences
2267 residues in 12 library sequences
- Tcomplib [36.3.8h Aug, 2019] (10 proc in memory [0G])
- start: Sun Jul 4 15:00:34 2021 done: Sun Jul 4 15:00:35 2021
- Total Scan time: 0.020 Total Display time: 0.030
+ Tcomplib [36.3.8h Aug, 2019] (18 proc in memory [0G])
+ start: Sun Aug 7 23:28:29 2022 done: Sun Aug 7 23:28:29 2022
+ Total Scan time: 0.000 Total Display time: 0.000
Function used was FASTA [36.3.8h Aug, 2019]
make[1]: Leaving directory '/build/fasta3-36.3.8h.2020-02-11'
@@ -3506,20 +3574,23 @@
dh_gencontrol -O--sourcedirectory=src
dh_md5sums -O--sourcedirectory=src
dh_builddeb -O--sourcedirectory=src
-dpkg-deb: building package 'fasta3-dbgsym' in '../fasta3-dbgsym_36.3.8h.2020-02-11-3_i386.deb'.
dpkg-deb: building package 'fasta3' in '../fasta3_36.3.8h.2020-02-11-3_i386.deb'.
+dpkg-deb: building package 'fasta3-dbgsym' in '../fasta3-dbgsym_36.3.8h.2020-02-11-3_i386.deb'.
dpkg-deb: building package 'fasta3-doc' in '../fasta3-doc_36.3.8h.2020-02-11-3_all.deb'.
dpkg-genbuildinfo --build=binary
dpkg-genchanges --build=binary >../fasta3_36.3.8h.2020-02-11-3_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)
+I: copying local configuration
+I: user script /srv/workspace/pbuilder/26194/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/26194/tmp/hooks/B01_cleanup finished
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
-I: removing directory /srv/workspace/pbuilder/15799 and its subdirectories
-I: Current time: Sun Jul 4 15:01:14 -12 2021
-I: pbuilder-time-stamp: 1625454074
+I: removing directory /srv/workspace/pbuilder/26194 and its subdirectories
+I: Current time: Sun Aug 7 23:28:37 +14 2022
+I: pbuilder-time-stamp: 1659864517