fasta3 →
36.3.8h.2020-02-11-3 →
armhf → 2020-04-20 08:32:56
sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on test2019
+==============================================================================+
| fasta3 36.3.8h.2020-02-11-3 (armhf) Mon, 20 Apr 2020 08:01:56 +0000 |
+==============================================================================+
Package: fasta3
Version: 36.3.8h.2020-02-11-3
Source Version: 36.3.8h.2020-02-11-3
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bullseye-staging-armhf-sbuild-9496d0d9-3096-4535-8b50-f2ad81878d7d' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.6 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.7 MB]
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Reading package lists...
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'fasta3' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/fasta3.git
Please use:
git clone https://salsa.debian.org/med-team/fasta3.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1271 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main fasta3 36.3.8h.2020-02-11-3 (dsc) [2192 B]
Get:2 http://172.17.0.1/private bullseye-staging/main fasta3 36.3.8h.2020-02-11-3 (tar) [1257 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main fasta3 36.3.8h.2020-02-11-3 (diff) [11.2 kB]
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Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/fasta3-iDZamj/fasta3-36.3.8h.2020-02-11' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/fasta3-iDZamj' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-D4bp65/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-D4bp65/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-D4bp65/gpg/trustdb.gpg: trustdb created
gpg: key E70254B6505CF8F7: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key E70254B6505CF8F7: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key E70254B6505CF8F7: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-D4bp65/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-D4bp65/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-D4bp65/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-D4bp65/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-D4bp65/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-D4bp65/apt_archive ./ Packages [433 B]
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Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-D4bp65/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-D4bp65/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY E70254B6505CF8F7
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
libpam-cap
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 3 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-D4bp65/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 12), libsimde-dev
Filtered Build-Depends: debhelper-compat (= 12), libsimde-dev
dpkg-deb: building package 'sbuild-build-depends-fasta3-dummy' in '/<<BUILDDIR>>/resolver-D4bp65/apt_archive/sbuild-build-depends-fasta3-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-fasta3-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-D4bp65/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-D4bp65/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-D4bp65/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-D4bp65/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-D4bp65/apt_archive ./ Sources [498 B]
Get:5 copy:/<<BUILDDIR>>/resolver-D4bp65/apt_archive ./ Packages [578 B]
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Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-D4bp65/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-D4bp65/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY E70254B6505CF8F7
Reading package lists...
Install fasta3 build dependencies (apt-based resolver)
------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
libpam-cap
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3
libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libglib2.0-0
libicu63 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsimde-dev
libsub-override-perl libtinfo5 libtool libuchardet0 libxml2 m4 man-db
po-debconf sensible-utils
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less
www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3
libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libglib2.0-0
libicu63 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsimde-dev
libsub-override-perl libtinfo5 libtool libuchardet0 libxml2 m4 man-db
po-debconf sbuild-build-depends-fasta3-dummy sensible-utils
0 upgraded, 37 newly installed, 0 to remove and 3 not upgraded.
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Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.2-1 [318 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-4 [783 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-2 [29.6 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.1-1 [1262 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-4 [262 kB]
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Get:12 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-4 [66.9 kB]
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Get:15 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-1 [775 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 12.10 [184 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
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Get:26 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.8.0-1 [14.8 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.64.1-1 [1157 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-3 [7987 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-4 [592 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.10 [1003 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libsimde-dev all 0.0.0.git.20200415-1 [85.4 kB]
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Setting up m4 (1.4.18-4) ...
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update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libcroco3:armhf (0.6.13-1) ...
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update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up gettext (0.19.8.1-10) ...
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Setting up intltool-debian (0.35.0+20060710.5) ...
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Setting up debhelper (12.10) ...
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Processing triggers for libc-bin (2.30-4+rpi1) ...
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.19.20-v7+ armhf (armv7l)
Toolchain package versions: binutils_2.34-5+rpi1 dpkg-dev_1.19.7 g++-9_9.3.0-10+rpi1 gcc-9_9.3.0-10+rpi1 libc6-dev_2.30-4+rpi1 libstdc++-9-dev_9.3.0-10+rpi1 libstdc++6_10-20200324-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_2.0.2 autoconf_2.69-11.1 automake_1:1.16.2-1 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-5+rpi1 binutils-arm-linux-gnueabihf_2.34-5+rpi1 binutils-common_2.34-5+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.3.0-10+rpi1 dash_0.5.10.2-7 debconf_1.5.73 debhelper_12.10 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.8.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.38-4 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.3.0-10+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-10-base_10-20200324-1+rpi1 gcc-9_9.3.0-10+rpi1 gcc-9-base_9.3.0-10+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-4 gzip_1.10-2 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-3 libacl1_2.2.53-6 libapt-pkg6.0_2.0.2 libarchive-zip-perl_1.68-1 libasan5_9.3.0-10+rpi1 libassuan0_2.5.3-7 libatomic1_10-20200324-1+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libbinutils_2.34-5+rpi1 libblkid1_2.34-0.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.30-4+rpi1 libc-dev-bin_2.30-4+rpi1 libc6_2.30-4+rpi1 libc6-dev_2.30-4+rpi1 libcap-ng0_0.7.9-2.1+b1 libcap2_1:2.33-1 libcap2-bin_1:2.33-1 libcc1-0_10-20200324-1+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libctf-nobfd0_2.34-5+rpi1 libctf0_2.34-5+rpi1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.251 libdebhelper-perl_12.10 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.8.0-1 libgcc-9-dev_9.3.0-10+rpi1 libgcc-s1_10-20200324-1+rpi1 libgcc1_1:10-20200324-1+rpi1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.1-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.13-2 libgomp1_10-20200324-1+rpi1 libgpg-error0_1.37-1 libhogweed5_3.5.1+really3.5.1-2 libicu63_63.2-3 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.49+dfsg-2 libldap-common_2.4.49+dfsg-3 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 libnpth0_1.6-1 libp11-kit0_0.23.20-1 libpam-cap_1:2.33-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12 libperl5.28_5.28.1-6 libperl5.30_5.30.0-9 libpipeline1_1.5.2-2 libreadline7_7.0-5 libreadline8_8.0-4 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+rpi1 libselinux1_3.0-1+b1 libsemanage-common_3.0-1 libsemanage1_3.0-1+b1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsimde-dev_0.0.0.git.20200415-1 libsmartcols1_2.34-0.1 libsqlite3-0_3.31.1-4 libss2_1.45.6-1 libstdc++-9-dev_9.3.0-10+rpi1 libstdc++6_10-20200324-1+rpi1 libsub-override-perl_0.09-2 libsystemd0_244.3-1+rpi1 libtasn1-6_4.16.0-2 libtinfo5_6.2-1 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10-20200324-1+rpi1 libuchardet0_0.0.6-3 libudev1_244.3-1+rpi1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml2_2.9.10+dfsg-4 libzstd1_1.4.4+dfsg-3+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.1-1 mawk_1.3.4.20200120-2 mount_2.34-0.1 ncurses-base_6.2-1 ncurses-bin_6.2-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.28_5.28.1-6 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 po-debconf_1.0.21 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-fasta3-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 tzdata_2019c-3 util-linux_2.34-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sat Apr 18 09:54:39 2020 UTC
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
dpkg-source: info: extracting fasta3 in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking fasta3_36.3.8h.2020-02-11.orig.tar.gz
dpkg-source: info: unpacking fasta3_36.3.8h.2020-02-11-3.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying Makefile.patch
dpkg-source: info: applying simde
dpkg-source: info: applying local_tests
dpkg-source: info: applying adjust-scripts
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INVOCATION_ID=720b06fe9d064e5ca4b0c1eb263ac862
JOURNAL_STREAM=8:20551
LANG=en_GB.UTF-8
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=116
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-9496d0d9-3096-4535-8b50-f2ad81878d7d
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_ID=c20708
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package fasta3
dpkg-buildpackage: info: source version 36.3.8h.2020-02-11-3
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean --sourcedirectory src
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
if [ -d src ]; then cd src && /usr/bin/make -f "../make/Makefile.linux64" clean-up; fi
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
rm -f *.o fasta36 ssearch36 lalign36 fasts36 fastx36 tfastx36 fasty36 tfasty36 tfasts36 fastm36 tfastm36 fastf36 tfastf36 glsearch36 ggsearch36 map_db; rm -rf ../bin/*
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_autoreconf_clean -O--sourcedirectory=src
dh_clean -O--sourcedirectory=src
debian/rules binary-arch
dh binary-arch --sourcedirectory src
dh_update_autotools_config -a -O--sourcedirectory=src
dh_autoreconf -a -O--sourcedirectory=src
dh_auto_configure -a -O--sourcedirectory=src
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build --sourcedirectory make --builddirectory src --buildsystem makefile -- -f "../make/Makefile.linux64"
cd src && make -j4 "INSTALL=install --strip-program=true" -f ../make/Makefile.linux64
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 pthr_subs2.c
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 compacc2e.c -o compacc2_t.o
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 mshowbest.c -o showbest.o
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 build_ares.c -o build_ares.o
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 re_getlib.c
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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
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",
| ~~^
| |
| long unsigned int
| %u
615 | nc,maxc,strlen(seqc0),strlen(seqc1));
| ~~~~~~~~~~~~~
| |
| size_t {aka unsigned int}
mshowalign2.c:614:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
614 | fprintf(stderr," mshowalign: nc/maxc: %d/%d seqc0/1: %lu/%lu\n",
| ~~^
| |
| long unsigned int
| %u
615 | nc,maxc,strlen(seqc0),strlen(seqc1));
| ~~~~~~~~~~~~~
| |
| size_t {aka unsigned int}
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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
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
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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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
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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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
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",
| ~~^
| |
| long int
| %d
404 | sizeof(struct lmf_str),lib_p->file_name);
| ~~~~~~~~~~~~~~~~~~~~~~
| |
| unsigned int
nmgetlib.c: In function 'sel_hacc_libstr_init':
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));
| ~~^ ~~~~~~~~~~~~~~~~~~~~
| | |
| long int unsigned int
| %d
nmgetlib.c:2032:54: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
2032 | fprintf(stderr, "cannot allocate acc_hash_link[%ld]\n",acc_cnt*sizeof(char *));
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~
| | |
| long int unsigned int
| %d
nmgetlib.c: In function 'sel_hacc_gi_init':
nmgetlib.c:2154:48: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
2154 | fprintf(stderr, "cannot allocate gi_hash[%ld]\n",hash_max*sizeof(int));
| ~~^ ~~~~~~~~~~~~~~~~~~~~
| | |
| long int unsigned int
| %d
nmgetlib.c:2160:53: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
2160 | fprintf(stderr, "cannot allocate gi_hash_link[%ld]\n",acc_cnt*sizeof(char *));
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~
| | |
| long int unsigned int
| %d
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c:623:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
623 | fgets(&lm_fd->lline[MAX_STR/2],MAX_STR/2,lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c:667:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
667 | fgets(&lm_fd->lline[strlen(lm_fd->lline)],MAX_STR-strlen(lm_fd->lline),lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c:682:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
682 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c: In function 'aranlib':
nmgetlib.c:702:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
702 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c: In function 'qgetlib':
nmgetlib.c:766:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
766 | fgets(&lm_fd->lline[strlen(lm_fd->lline)],MAX_STR/2,lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c:768:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
768 | fgets(&lm_fd->lline[MAX_STR/2],MAX_STR/2,lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c:800:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
800 | fgets(&lm_fd->lline[strlen(lm_fd->lline)],MAX_STR-strlen(lm_fd->lline),lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c: In function 'qranlib':
nmgetlib.c:823:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
823 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c: In function 'lgetlib':
nmgetlib.c:878:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
878 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c:916:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
916 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c: In function 'lget_ann':
nmgetlib.c:940:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
940 | fgets(desc,sizeof(desc),lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c:942:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
942 | fgets(desc,sizeof(desc),lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c:946:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
946 | fgets(acc,sizeof(acc),lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c:948:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
948 | fgets(acc,sizeof(acc),lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c:956:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
956 | fgets(ver,sizeof(ver),lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c:958:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
958 | fgets(ver,sizeof(ver),lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c: In function 'lranlib':
nmgetlib.c:1032:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
1032 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c:1039:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
1039 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c: In function 'pgetlib':
nmgetlib.c:1078:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
1078 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); /* get the extra line */
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c:1100:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
1100 | 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=/<<PKGBUILDDIR>>=. -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
nmgetlib.c: In function 'pranlib':
nmgetlib.c:1124:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
1124 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c:1128:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
1128 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c:1130:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
1130 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c:1136:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
1136 | 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=/<<PKGBUILDDIR>>=. -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 'egetlib':
nmgetlib.c:1220:1: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
1220 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c: In function 'eranlib':
nmgetlib.c:1250:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
1250 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c:1255:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
1255 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c:1258:56: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
1258 | while (lm_fd->lline[0]!='D' || lm_fd->lline[1]!='E') fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c:1265:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
1265 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c: In function 'igetlib':
nmgetlib.c:1297:32: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
1297 | while (lm_fd->lline[0]==';') fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c:1329:6: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
1329 | fgets(lm_fd->lline,MAX_STR-strlen(lm_fd->lline),lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c:1333:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
1333 | 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=/<<PKGBUILDDIR>>=. -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: In function 'iranlib':
nmgetlib.c:1360:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
1360 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c:1371:31: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
1371 | while (lm_fd->lline[0]==';') fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c:1380:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
1380 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c: In function 'vgetlib':
nmgetlib.c:1419:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
1419 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c:1459:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
1459 | fgets(&lm_fd->lline[strlen(lm_fd->lline)],MAX_STR-strlen(lm_fd->lline),lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c:1508:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
1508 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c:1525:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
1525 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c: In function 'gcg_getlib':
nmgetlib.c:1567:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
1567 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c:1592:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1592 | fread((char *)seqp,(size_t)r_block,(size_t)1,lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c:1607:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
1607 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c: In function 'gcg_ranlib':
nmgetlib.c:1631:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
1631 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nmgetlib.c:1641:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
1641 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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",
| ~~^
| |
| long int
| %d
1434 | libstr,*libpos,tmp,seqcnt,*seq);
| ~~~
| |
| size_t {aka unsigned int}
ncbl2_mlib.c:1453:58: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1453 | fprintf(stderr," could not read sequence record: %lld %ld/%ld\n",
| ~~^
| |
| long int
| %d
1454 | *libpos,tmp,seqcnt);
| ~~~
| |
| size_t {aka unsigned int}
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",
| ~~^
| |
| long int
| %d
1594 | __FILE__, __LINE__, amb_cnt * sizeof(unsigned int));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| unsigned int
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ncbl2_mlib.c:820:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
820 | fread(pdb_title_str,(size_t)1,(size_t)pdb_title_len,ifile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ncbl2_mlib.c:831:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
831 | fread(date_str,(size_t)1,(size_t)date_len,ifile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ncbl2_mlib.c: In function 'ncbl2_ranlib':
ncbl2_mlib.c:1719:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1719 | fread(str,(size_t)1,(size_t)(llen),m_fd->hfile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ncbl2_mlib.c:1734:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1734 | fread(my_buff,(size_t)1,llen,m_fd->hfile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ncbl2_mlib.c: In function 'src_int4_read':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ncbl2_mlib.c: In function 'src_uint4_read':
ncbl2_mlib.c:1868:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1868 | fread((char *)&b[0],(size_t)1,(size_t)4,fd);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ncbl2_mlib.c: In function 'src_long8_read':
ncbl2_mlib.c:1883:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1883 | fread((char *)&b[0],(size_t)1,(size_t)8,fd);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ncbl2_mlib.c: In function 'ncbi_long8_read':
ncbl2_mlib.c:1903:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1903 | fread((char *)&b[0],(size_t)1,(size_t)8,fd);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ncbl2_mlib.c: In function 'src_char_read':
ncbl2_mlib.c:1910:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1910 | fread(val,(size_t)1,(size_t)1,fd);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ncbl2_mlib.c: In function 'src_fstr_read':
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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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
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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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
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",
| ~~^
| |
| long unsigned int
| %u
615 | nc,maxc,strlen(seqc0),strlen(seqc1));
| ~~~~~~~~~~~~~
| |
| size_t {aka unsigned int}
mshowalign2.c:614:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
614 | fprintf(stderr," mshowalign: nc/maxc: %d/%d seqc0/1: %lu/%lu\n",
| ~~^
| |
| long unsigned int
| %u
615 | nc,maxc,strlen(seqc0),strlen(seqc1));
| ~~~~~~~~~~~~~
| |
| size_t {aka 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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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
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=]
994 | fprintf(stderr,"Ran out of near memory: %ld*%ld/%ld\n",amount,size,mtotal);
| ~~^ ~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
lsim4.c:994:51: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
994 | fprintf(stderr,"Ran out of near memory: %ld*%ld/%ld\n",amount,size,mtotal);
| ~~^ ~~~~
| | |
| long int size_t {aka unsigned int}
| %d
lsim4.c:994:55: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
994 | fprintf(stderr,"Ran out of near memory: %ld*%ld/%ld\n",amount,size,mtotal);
| ~~^ ~~~~~~
| | |
| long int size_t {aka 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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 scaleswt.c -o scaleswts.o
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
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
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));
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| | unsigned int
| long int
| %d
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));
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| | unsigned int
| long int
| %d
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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
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",
| ~~^
| |
| long int
| %d
378 | tat_size * sizeof(struct tat_str *));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| unsigned int
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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
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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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
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]",
| ~~^
| |
| long unsigned int
| %u
2661 | __FILE__, __LINE__, sizeof(struct a_res_str));
| ~~~~~~~~~~~~~~~~~~~~~~~~
| |
| unsigned int
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
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]",
| ~~^
| |
| long unsigned int
| %u
2661 | __FILE__, __LINE__, sizeof(struct a_res_str));
| ~~~~~~~~~~~~~~~~~~~~~~~~
| |
| unsigned int
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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
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':
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]",
| ~~^
| |
| long unsigned int
| %u
2673 | __FILE__, __LINE__, sizeof(struct a_res_str));
| ~~~~~~~~~~~~~~~~~~~~~~~~
| |
| 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=/<<PKGBUILDDIR>>=. -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
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':
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]",
| ~~^
| |
| long unsigned int
| %u
2673 | __FILE__, __LINE__, sizeof(struct a_res_str));
| ~~~~~~~~~~~~~~~~~~~~~~~~
| |
| unsigned int
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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));
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long int unsigned int
| %d
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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
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",
| ~~^
| |
| long int
| %d
378 | tat_size * sizeof(struct tat_str *));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| unsigned int
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
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",
| ~~^
| |
| long int
| %d
378 | tat_size * sizeof(struct tat_str *));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| unsigned int
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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
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",
| ~~^
| |
| long unsigned int
| %u
615 | nc,maxc,strlen(seqc0),strlen(seqc1));
| ~~~~~~~~~~~~~
| |
| size_t {aka unsigned int}
mshowalign2.c:614:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
614 | fprintf(stderr," mshowalign: nc/maxc: %d/%d seqc0/1: %lu/%lu\n",
| ~~^
| |
| long unsigned int
| %u
615 | nc,maxc,strlen(seqc0),strlen(seqc1));
| ~~~~~~~~~~~~~
| |
| size_t {aka 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=/<<PKGBUILDDIR>>=. -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
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",
| ~~^
| |
| long int
| %d
378 | tat_size * sizeof(struct tat_str *));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| unsigned int
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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
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));
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| | unsigned int
| long int
| %d
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));
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| | unsigned int
| long int
| %d
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",
| ~~^
| |
| long unsigned int
| %u
121 | __FILE__, __LINE__, sizeof(struct f_struct));
| ~~~~~~~~~~~~~~~~~~~~~~~
| |
| unsigned int
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]",
| ~~^
| |
| long unsigned int
| %u
1177 | __FILE__, __LINE__, sizeof(struct a_res_str));
| ~~~~~~~~~~~~~~~~~~~~~~~~
| |
| unsigned int
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 cal_consf.c -o calcons_ff.o
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 initfa.c -o init_tf.o
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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
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
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",
| ~~^
| |
| long unsigned int
| %u
121 | __FILE__, __LINE__, sizeof(struct f_struct));
| ~~~~~~~~~~~~~~~~~~~~~~~
| |
| unsigned int
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]",
| ~~^
| |
| long unsigned int
| %u
1177 | __FILE__, __LINE__, sizeof(struct a_res_str));
| ~~~~~~~~~~~~~~~~~~~~~~~~
| |
| unsigned int
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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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
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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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
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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
map_db.c: In function 'gbf_get_ent':
map_db.c:512:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
512 | fgets(lline,MAXLINE,libf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
map_db.c: In function 'src_int4_read':
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/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
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
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 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/arm-linux-gnueabihf/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' at mshowalign2.c:577:8:
/usr/include/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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,
inlined from 'initenv' at doinit.c:359:4:
/usr/include/arm-linux-gnueabihf/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 'initenv':
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:
/usr/include/arm-linux-gnueabihf/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 'initenv':
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/arm-linux-gnueabihf/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/fasts36.3cMrk9.ltrans3.ltrans.o: in function `main':
/<<PKGBUILDDIR>>/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/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
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 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/arm-linux-gnueabihf/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' at mshowalign2.c:577:8:
/usr/include/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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,
inlined from 'initenv' at doinit.c:359:4:
/usr/include/arm-linux-gnueabihf/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 'initenv':
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:
/usr/include/arm-linux-gnueabihf/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 'initenv':
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/arm-linux-gnueabihf/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/fasta36.tcBfUr.ltrans4.ltrans.o: in function `main':
/<<PKGBUILDDIR>>/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/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
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 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/arm-linux-gnueabihf/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' at mshowalign2.c:577:8:
/usr/include/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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) {
| ^
/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 'alloc_file_name' at nmgetlib.c:2274:5,
inlined from 'open_lib' at nmgetlib.c:390:26:
/usr/include/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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 '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:
/usr/include/arm-linux-gnueabihf/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 'initenv':
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:
/usr/include/arm-linux-gnueabihf/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 'initenv':
doinit.c:785:5: note: length computed here
785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1));
| ^
/usr/bin/ld: /tmp/ssearch36.6JehIG.ltrans5.ltrans.o: in function `main':
/<<PKGBUILDDIR>>/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/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
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
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 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/arm-linux-gnueabihf/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' at mshowalign2.c:577:8:
/usr/include/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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) {
| ^
/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 'alloc_file_name' at nmgetlib.c:2274:5,
inlined from 'open_lib' at nmgetlib.c:390:26:
/usr/include/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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,
inlined from 'initenv' at doinit.c:359:4:
/usr/include/arm-linux-gnueabihf/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 'initenv':
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:
/usr/include/arm-linux-gnueabihf/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 'initenv':
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/arm-linux-gnueabihf/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/lalign36.4Chrgk.ltrans4.ltrans.o: in function `main':
/<<PKGBUILDDIR>>/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/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
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 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/arm-linux-gnueabihf/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' at mshowalign2.c:577:8:
/usr/include/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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 '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:
/usr/include/arm-linux-gnueabihf/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 'initenv':
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:
/usr/include/arm-linux-gnueabihf/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 'initenv':
doinit.c:785:5: note: length computed here
785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1));
| ^
/usr/bin/ld: /tmp/fastx36.khStpk.ltrans4.ltrans.o: in function `main':
/<<PKGBUILDDIR>>/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/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)
| ^
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 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/arm-linux-gnueabihf/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' at mshowalign2.c:577:8:
/usr/include/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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 '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:
/usr/include/arm-linux-gnueabihf/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 'initenv':
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:
/usr/include/arm-linux-gnueabihf/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 'initenv':
doinit.c:785:5: note: length computed here
785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1));
| ^
/usr/bin/ld: /tmp/tfastx36.nRAs0s.ltrans3.ltrans.o: in function `main':
/<<PKGBUILDDIR>>/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/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)
| ^
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 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/arm-linux-gnueabihf/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' at mshowalign2.c:577:8:
/usr/include/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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 '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:
/usr/include/arm-linux-gnueabihf/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 'initenv':
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:
/usr/include/arm-linux-gnueabihf/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 'initenv':
doinit.c:785:5: note: length computed here
785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1));
| ^
/usr/bin/ld: /tmp/fasty36.lIlTOT.ltrans4.ltrans.o: in function `main':
/<<PKGBUILDDIR>>/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/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
In function 'strncpy',
inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/arm-linux-gnueabihf/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' at mshowalign2.c:577:8:
/usr/include/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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 '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:
/usr/include/arm-linux-gnueabihf/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 'initenv':
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:
/usr/include/arm-linux-gnueabihf/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 'initenv':
doinit.c:785:5: note: length computed here
785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1));
| ^
/usr/bin/ld: /tmp/tfasty36.ogRiSi.ltrans4.ltrans.o: in function `main':
/<<PKGBUILDDIR>>/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
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 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/arm-linux-gnueabihf/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' at mshowalign2.c:577:8:
/usr/include/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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,
inlined from 'initenv' at doinit.c:359:4:
/usr/include/arm-linux-gnueabihf/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 'initenv':
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:
/usr/include/arm-linux-gnueabihf/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 'initenv':
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/arm-linux-gnueabihf/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/tfasts36.rS683m.ltrans3.ltrans.o: in function `main':
/<<PKGBUILDDIR>>/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/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
In function 'strncpy',
inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/arm-linux-gnueabihf/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' at mshowalign2.c:577:8:
/usr/include/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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,
inlined from 'initenv' at doinit.c:359:4:
/usr/include/arm-linux-gnueabihf/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 'initenv':
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:
/usr/include/arm-linux-gnueabihf/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 'initenv':
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/arm-linux-gnueabihf/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/fastm36.ekeXiu.ltrans3.ltrans.o: in function `main':
/<<PKGBUILDDIR>>/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
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 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/arm-linux-gnueabihf/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' at mshowalign2.c:577:8:
/usr/include/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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,
inlined from 'initenv' at doinit.c:359:4:
/usr/include/arm-linux-gnueabihf/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 'initenv':
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:
/usr/include/arm-linux-gnueabihf/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 'initenv':
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/arm-linux-gnueabihf/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/fastf36.EyS0U5.ltrans3.ltrans.o: in function `main':
/<<PKGBUILDDIR>>/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
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
In function 'strncpy',
inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/arm-linux-gnueabihf/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' at mshowalign2.c:577:8:
/usr/include/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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,
inlined from 'initenv' at doinit.c:359:4:
/usr/include/arm-linux-gnueabihf/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 'initenv':
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:
/usr/include/arm-linux-gnueabihf/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 'initenv':
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/arm-linux-gnueabihf/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/tfastm36.LsyDfp.ltrans3.ltrans.o: in function `main':
/<<PKGBUILDDIR>>/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
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 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/arm-linux-gnueabihf/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' at mshowalign2.c:577:8:
/usr/include/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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,
inlined from 'initenv' at doinit.c:359:4:
/usr/include/arm-linux-gnueabihf/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 'initenv':
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:
/usr/include/arm-linux-gnueabihf/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 'initenv':
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/arm-linux-gnueabihf/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/tfastf36.GprAOA.ltrans3.ltrans.o: in function `main':
/<<PKGBUILDDIR>>/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
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 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/arm-linux-gnueabihf/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' at mshowalign2.c:577:8:
/usr/include/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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) {
| ^
/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 'alloc_file_name' at nmgetlib.c:2274:5,
inlined from 'open_lib' at nmgetlib.c:390:26:
/usr/include/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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,
inlined from 'initenv' at doinit.c:359:4:
/usr/include/arm-linux-gnueabihf/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 'initenv':
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:
/usr/include/arm-linux-gnueabihf/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 'initenv':
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/arm-linux-gnueabihf/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/glsearch36.vDZR8H.ltrans5.ltrans.o: in function `main':
/<<PKGBUILDDIR>>/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
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 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/arm-linux-gnueabihf/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' at mshowalign2.c:577:8:
/usr/include/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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) {
| ^
/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 'alloc_file_name' at nmgetlib.c:2274:5,
inlined from 'open_lib' at nmgetlib.c:390:26:
/usr/include/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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,
inlined from 'initenv' at doinit.c:359:4:
/usr/include/arm-linux-gnueabihf/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 'initenv':
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:
/usr/include/arm-linux-gnueabihf/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 'initenv':
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/arm-linux-gnueabihf/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/ggsearch36.AMlqCI.ltrans5.ltrans.o: in function `main':
/<<PKGBUILDDIR>>/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
# convoluted, but necessary to allow cross builds
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cd test ; ./test2G.sh && ./test.sh && ../bin/fasta36 -q ../seq/mgstm1.aa ../seq/prot_test.lseg
STARTING FASTA36 Mon Apr 20 08:14:48 UTC 2020 on test2019
Linux test2019 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armv7l GNU/Linux
starting prss36(ssearch/fastx) Mon Apr 20 08:14:48 UTC 2020
done
starting lalign36 Mon Apr 20 08:14:50 UTC 2020
FINISHED Mon Apr 20 08:23:16 UTC 2020
STARTING FASTA36 Mon Apr 20 08:23:16 UTC 2020 on test2019
Linux test2019 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armv7l GNU/Linux
starting prss36(ssearch/fastx) Mon Apr 20 08:23:16 UTC 2020
done
starting lalign36 Mon Apr 20 08:23:17 UTC 2020
FINISHED Mon Apr 20 08:31:49 UTC 2020
# ../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
Please cite:
W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448
Query: ../seq/mgstm1.aa
1>>>sp|P10649|GSTM1_MOUSE Glutathione S-transferase Mu 1; GST 1-1; GST class-mu 1; Glutathione S-transferase GT8.7; pmGT10 - 218 aa
Library: ../seq/prot_test.lseg
2267 residues in 12 sequences
Statistics: (shuffled [466]) MLE statistics: Lambda= 0.1679; K=0.005609
statistics sampled from 4 (4) to 465 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: 0.040
The best scores are: opt bits E(12)
sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu ( 218) 1242 310.2 2.3e-88
sp|P00502|GSTA1_RAT Glutathione S-transferase alph ( 222) 237 66.8 4.5e-15
sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Ho ( 142) 51 21.8 0.1
sp|P00517|KAPCA_BOVIN cAMP-dependent protein kinas ( 351) 43 19.8 0.95
sp|P14960|RBS_GUITH Ribulose bisphosphate carboxyl ( 139) 36 18.1 1.2
sp|P01593|KV101_HUMAN Ig kappa chain V-I region AG ( 108) 31 16.9 2.1
sp|P99998|CYC_PANTR Cytochrome c OS=Pan troglodyte ( 105) 30 16.7 2.4
sp|P02585|TNNC2_HUMAN Troponin C, skeletal muscle ( 160) 30 16.7 3.4
sp|P03435|HEMA_I75A3 Hemagglutinin OS=Influenza A ( 567) 37 18.4 3.7
sp|P60615|NXL1A_BUNMU Alpha-bungarotoxin isoform A ( 95) 26 15.7 3.8
sp|P00193|FER_PEPAS Ferredoxin OS=Peptostreptococc ( 54) 22 14.7 4.2
sp|P01834|IGKC_HUMAN Ig kappa chain C region OS=Ho ( 106) 23 15.0 6.1
>>sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu 1 O (218 aa)
initn: 1242 init1: 1242 opt: 1242 Z-score: 1638.1 bits: 310.2 E(12): 2.3e-88
Smith-Waterman score: 1242; 78.0% identity (95.4% similar) in 218 aa overlap (1-218:1-218)
10 20 30 40 50 60
sp|P10 MPMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKFKLGLDFPNL
::::::::..:::.: ::.:::::::::.::.::::::::.:::::::::::::::::::
sp|P09 MPMILGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNL
10 20 30 40 50 60
70 80 90 100 110 120
sp|P10 PYLIDGSHKITQSNAILRYLARKHHLDGETEEERIRADIVENQVMDTRMQLIMLCYNPDF
::::::.:::::::::: :.::::.: ::::::.::.::.:::.::..::: :.::::.:
sp|P09 PYLIDGAHKITQSNAILCYIARKHNLCGETEEEKIRVDILENQTMDNHMQLGMICYNPEF
70 80 90 100 110 120
130 140 150 160 170 180
sp|P10 EKQKPEFLKTIPEKMKLYSEFLGKRPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPN
:: ::..:. .:::.:::::::::::::::.:.:.::::.::.:: .:.:::::::::::
sp|P09 EKLKPKYLEELPEKLKLYSEFLGKRPWFAGNKITFVDFLVYDVLDLHRIFEPKCLDAFPN
130 140 150 160 170 180
190 200 210
sp|P10 LRDFLARFEGLKKISAYMKSSRYIATPIFSKMAHWSNK
:.::..:::::.::::::::::.. :.::::: :.::
sp|P09 LKDFISRFEGLEKISAYMKSSRFLPRPVFSKMAVWGNK
190 200 210
>>sp|P00502|GSTA1_RAT Glutathione S-transferase alpha-1 (222 aa)
initn: 204 init1: 73 opt: 237 Z-score: 322.5 bits: 66.8 E(12): 4.5e-15
Smith-Waterman score: 237; 27.4% identity (57.0% similar) in 223 aa overlap (4-218:6-218)
10 20 30 40 50
sp|P10 MPMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKFKL--GLD
.: :.:.:: . :: :: . .::: : .: ::.: .:
sp|P00 MSGKPVLHYFNARGRMECIRWLLAAAGVEFDEK---------FIQSPEDLEKLKKDGNLM
10 20 30 40 50
60 70 80 90 100 110
sp|P10 FPNLPYL-IDGSHKITQSNAILRYLARKHHLDGETEEERIRADIVENQVMD-TRMQLIML
: ..:.. ::: :..:. ::: :.: :. : :. .:: :. . ..: :.: . ..
sp|P00 FDQVPMVEIDG-MKLAQTRAILNYIATKYDLYGKDMKERALIDMYTEGILDLTEMIMQLV
60 70 80 90 100 110
120 130 140 150 160 170
sp|P10 CYNPDFEKQKPEFLK--TIPEKMKLYSEFLGK--RPWFAGDKVTYVDFLAYDILDQYRMF
:: .. : . : : . . . . : . . ...:...: ::. ..: . :
sp|P00 ICPPDQKEAKTALAKDRTKNRYLPAFEKVLKSHGQDYLVGNRLTRVDIHLLELLLYVEEF
120 130 140 150 160 170
180 190 200 210
sp|P10 EPKCLDAFPNLRDFLARFEGLKKISAYMKSSRYIATPIFSKMAHWSNK
. . : .:: :. : .:. .: ... ... . :. .:. . . :
sp|P00 DASLLTSFPLLKAFKSRISSLPNVKKFLQPGSQRKLPVDAKQIEEARKIFKF
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: 82.5 bits: 21.8 E(12): 0.1
Smith-Waterman score: 51; 25.6% identity (69.2% similar) in 39 aa overlap (177-214:36-73)
150 160 170 180 190 200
sp|P10 WFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKS-SRYIA
.::. . .. .:. :.. :: .:. .. .:
sp|P69 ADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFD-LSHGSAQVKGHGKKVA
10 20 30 40 50 60
210
sp|P10 TPIFSKMAHWSNK
. . .::
sp|P69 DALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHA
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: 65.0 bits: 19.8 E(12): 0.95
Smith-Waterman score: 54; 23.6% identity (47.2% similar) in 72 aa overlap (137-206:229-300)
110 120 130 140 150 160
sp|P10 TRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAGDKVTYVDFLAYDILDQ
.: : :.:: . . . .. .
sp|P00 LCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRF
200 210 220 230 240 250
170 180 190 200 210
sp|P10 YRMFEPKCLDAFPNLR--DFLARFEGLKKISAYMKSSRYIATPIFSKMAHWSNK
: : . :: :. :: .::. .:. ...::
sp|P00 PSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPK
260 270 280 290 300 310
sp|P00 FKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF
320 330 340 350
>>sp|P14960|RBS_GUITH Ribulose bisphosphate carboxylase (139 aa)
initn: 56 init1: 36 opt: 36 Z-score: 63.0 bits: 18.1 E(12): 1.2
Smith-Waterman score: 36; 57.1% identity (85.7% similar) in 7 aa overlap (7-13:47-53)
10 20 30
sp|P10 MPMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMG
::.. ::
sp|P14 EQIVKQIQYAISKNWALNVEWTDDPHPRNAYWDLWGLPLFGIKDPAAVMFEINACRKAKP
20 30 40 50 60 70
40 50 60 70 80 90
sp|P10 DAPDFDRSQWLNEKFKLGLDFPNLPYLIDGSHKITQSNAILRYLARKHHLDGETEEERIR
sp|P14 ACYVKVNAFDNSRGVESCCLSFIVQRPTSNEPGFQLIRSEVDSRNIRYTIQSYASTRPEG
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: 58.5 bits: 16.9 E(12): 2.1
Smith-Waterman score: 33; 36.0% identity (54.0% similar) in 50 aa overlap (150-190:16-64)
120 130 140 150 160 170
sp|P10 FEKQKPEFLKTIPEKMKLYSEFLGKRPWFAGDKVTYVDFLAYDI---LDQYRMFE---PK
::.:: . . :: :. :.. ::
sp|P01 DIQMTQSPSSLSASVGDRVTITCQASQDINHYLNWYQQGPKKAPK
10 20 30 40
180 190 200 210
sp|P10 CL--DAFPNLRDFL-ARFEGLKKISAYMKSSRYIATPIFSKMAHWSNK
: :: ::. . .:: :
sp|P01 ILIYDA-SNLETGVPSRFSGSGFGTDFTFTISGLQPEDIATYYCQQYDTLPRTFGQGTKL
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: 57.4 bits: 16.7 E(12): 2.4
Smith-Waterman score: 36; 26.5% identity (54.4% similar) in 68 aa overlap (129-193:28-88)
100 110 120 130 140 150
sp|P10 IVENQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWF---AGDKVTY
:: :. :... :. : . :..:
sp|P99 MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKG
10 20 30 40 50
160 170 180 190 200 210
sp|P10 VDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRYIATPIFSKMAHW
. . . : : .: . .:: .:. . . : :.::
sp|P99 I-IWGEDTLMEY-LENPK--KYIPGTKMI---FVGIKKKEERADLIAYLKKATNE
60 70 80 90 100
sp|P10 SNK
>>sp|P02585|TNNC2_HUMAN Troponin C, skeletal muscle OS=H (160 aa)
initn: 30 init1: 30 opt: 30 Z-score: 54.1 bits: 16.7 E(12): 3.4
Smith-Waterman score: 41; 25.9% identity (63.0% similar) in 54 aa overlap (44-92:13-62)
20 30 40 50 60 70
sp|P10 THPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKFKLGLDFPNLPYLIDGSHKIT--
:. . .:: ..:. . ::. :.
sp|P02 MTDQQAEARSYLSEEMIAEFKAAFDM----FDADGGGDISVK
10 20 30
80 90 100 110 120
sp|P10 QSNAILRYLAR---KHHLDGETEEERIRADIVENQVMDTRMQLIMLCYNPDFEKQKPEFL
. ....:.:.. :..::. ::
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: 53.4 bits: 18.4 E(12): 3.7
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: 52.9 bits: 15.7 E(12): 3.8
Smith-Waterman score: 30; 54.5% identity (63.6% similar) in 11 aa overlap (115-125:86-94)
90 100 110 120 130 140
sp|P10 HLDGETEEERIRADIVENQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGK
: :: ::.:
sp|P60 SRGKVVELGCAATCPSKKPYEEVTCCSTDKC-NPH-PKQRPG
60 70 80 90
150 160 170 180 190 200
sp|P10 RPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRYI
>>sp|P00193|FER_PEPAS Ferredoxin OS=Peptostreptococcus a (54 aa)
initn: 22 init1: 22 opt: 22 Z-score: 52.1 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
sp|P10 FLGKRPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKS
.:.:
sp|P00 AYVINDSCIACGACKPECPVNIQQGSIYAIDADSCIDCGSCASV
10 20 30 40
210
sp|P10 SRYIATPIFSKMAHWSNK
sp|P00 CPVGAPNPED
50
>>sp|P01834|IGKC_HUMAN Ig kappa chain C region OS=Homo s (106 aa)
initn: 23 init1: 23 opt: 23 Z-score: 48.1 bits: 15.0 E(12): 6.1
Smith-Waterman score: 35; 18.3% identity (53.5% similar) in 71 aa overlap (58-124:12-82)
30 40 50 60 70 80
sp|P10 YDEKRYTMGDAPDFDRSQWLNEKFKLGLDFPNLPYLIDGSHKIT--QSNAILRYLARKHH
:. : .:. ... .: : . .
sp|P01 TVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWK
10 20 30 40
90 100 110 120 130 140
sp|P10 LDGETEEERIRADIVENQVMDTRMQL--IMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLG
.:. . . ...:.. :. ..: . . :.::.:
sp|P01 VDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSF
50 60 70 80 90 100
150 160 170 180 190 200
sp|P10 KRPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRY
sp|P01 NRGEC
218 residues in 1 query sequences
2267 residues in 12 library sequences
Tcomplib [36.3.8h Aug, 2019] (4 proc in memory [0G])
start: Mon Apr 20 08:31:49 2020 done: Mon Apr 20 08:31:49 2020
Total Scan time: 0.040 Total Display time: 0.030
Function used was FASTA [36.3.8h Aug, 2019]
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
dh_testroot -a -O--sourcedirectory=src
dh_prep -a -O--sourcedirectory=src
dh_auto_install -a -O--sourcedirectory=src
dh_install -a -O--sourcedirectory=src
dh_installdocs -a -O--sourcedirectory=src
dh_installchangelogs -a -O--sourcedirectory=src
dh_installexamples -a -O--sourcedirectory=src
dh_installman -a -O--sourcedirectory=src
dh_installinit -a -O--sourcedirectory=src
dh_installsystemduser -a -O--sourcedirectory=src
dh_perl -a -O--sourcedirectory=src
dh_link -a -O--sourcedirectory=src
dh_strip_nondeterminism -a -O--sourcedirectory=src
debian/rules override_dh_compress
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_compress --exclude=.pdf
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_fixperms -a -O--sourcedirectory=src
dh_missing -a -O--sourcedirectory=src
dh_dwz -a -O--sourcedirectory=src
dh_strip -a -O--sourcedirectory=src
dh_makeshlibs -a -O--sourcedirectory=src
dh_shlibdeps -a -O--sourcedirectory=src
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/fasta3/usr/bin/tfastx36 debian/fasta3/usr/bin/map_db debian/fasta3/usr/bin/ggsearch36 debian/fasta3/usr/bin/fastx36 debian/fasta3/usr/bin/tfastm36 debian/fasta3/usr/bin/glsearch36 debian/fasta3/usr/bin/lalign36 debian/fasta3/usr/bin/tfasts36 debian/fasta3/usr/bin/tfasty36 debian/fasta3/usr/bin/fasty36 debian/fasta3/usr/bin/fastm36 debian/fasta3/usr/bin/ssearch36 debian/fasta3/usr/bin/tfastf36 debian/fasta3/usr/bin/fasts36 debian/fasta3/usr/bin/fasta36 debian/fasta3/usr/bin/fastf36 were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a -O--sourcedirectory=src
dh_gencontrol -a -O--sourcedirectory=src
dh_md5sums -a -O--sourcedirectory=src
dh_builddeb -a -O--sourcedirectory=src
dpkg-deb: building package 'fasta3' in '../fasta3_36.3.8h.2020-02-11-3_armhf.deb'.
dpkg-deb: building package 'fasta3-dbgsym' in '../fasta3-dbgsym_36.3.8h.2020-02-11-3_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian 2019 test autobuilder <root@raspbian.org> >../fasta3_36.3.8h.2020-02-11-3_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2020-04-20T08:32:32Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
fasta3_36.3.8h.2020-02-11-3_armhf.changes:
------------------------------------------
Format: 1.8
Date: Sat, 18 Apr 2020 11:46:22 +0200
Source: fasta3
Binary: fasta3 fasta3-dbgsym
Architecture: armhf
Version: 36.3.8h.2020-02-11-3
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian 2019 test autobuilder <root@raspbian.org>
Changed-By: Michael R. Crusoe <michael.crusoe@gmail.com>
Description:
fasta3 - tools for searching collections of biological sequences
Changes:
fasta3 (36.3.8h.2020-02-11-3) unstable; urgency=medium
.
* Team upload.
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)
* debian/upstream/metadata: added Repository{,-Browse}
* Enable buildiing on non-X86 via SIMD Everywhere library
* fasta3-doc: Multi-Arch: foreign
* Enable cross building
* Improve hardening
* drop unneeded build-dep on zlib1g-dev
* Add autopkgtests
* Install scripts/ to usr/share/fasta3/
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fasta3-dbgsym_36.3.8h.2020-02-11-3_armhf.deb
--------------------------------------------
new Debian package, version 2.0.
size 5174552 bytes: control archive=1336 bytes.
1008 bytes, 12 lines control
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Package: fasta3-dbgsym
Source: fasta3
Version: 36.3.8h.2020-02-11-3
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5700
Depends: fasta3 (= 36.3.8h.2020-02-11-3)
Section: debug
Priority: optional
Description: debug symbols for fasta3
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fasta3_36.3.8h.2020-02-11-3_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 619756 bytes: control archive=3380 bytes.
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5272 bytes, 81 lines md5sums
Package: fasta3
Version: 36.3.8h.2020-02-11-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5096
Depends: libc6 (>= 2.29)
Suggests: perl:any, libdbi-perl, libwww-perl, libjson-perl, libhtml-tableextract-perl, libxml-twig-perl, liburi-encode-perl, libdbd-mysql-perl, python3-mysqldb, ncbi-blast+, bedtools
Section: science
Priority: optional
Homepage: https://fasta.bioch.virginia.edu
Description: tools for searching collections of biological sequences
The FASTA programs find regions of local or global similarity between
Protein or DNA sequences, either by searching Protein or DNA databases,
or by identifying local duplications within a sequence. Other
programs provide information on the statistical significance of an
alignment. Like BLAST, FASTA can be used to infer functional and
evolutionary relationships between sequences as well as help identify
members of gene families.
.
* Protein
- Protein-protein FASTA
- Protein-protein Smith-Waterman (ssearch)
- Global Protein-protein (Needleman-Wunsch) (ggsearch)
- Global/Local protein-protein (glsearch)
- Protein-protein with unordered peptides (fasts)
- Protein-protein with mixed peptide sequences (fastf)
.
* Nucleotide
- Nucleotide-Nucleotide (DNA/RNA fasta)
- Ordered Nucleotides vs Nucleotide (fastm)
- Un-ordered Nucleotides vs Nucleotide (fasts)
.
* Translated
- Translated DNA (with frameshifts, e.g. ESTs)
vs Proteins (fastx/fasty)
- Protein vs Translated DNA (with frameshifts)
(tfastx/tfasty)
- Peptides vs Translated DNA (tfasts)
.
* Statistical Significance
- Protein vs Protein shuffle (prss)
- DNA vs DNA shuffle (prss)
- Translated DNA vs Protein shuffle (prfx)
.
* Local Duplications
- Local Protein alignments (lalign)
- Plot Protein alignment "dot-plot" (plalign)
- Local DNA alignments (lalign)
- Plot DNA alignment "dot-plot" (plalign)
.
This software is often used via a web service at the
EBI with readily indexed reference databases at
http://www.ebi.ac.uk/Tools/fasta/.
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| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build Type: any
Build-Space: 55780
Build-Time: 1491
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 287
Job: fasta3_36.3.8h.2020-02-11-3
Machine Architecture: armhf
Package: fasta3
Package-Time: 1836
Source-Version: 36.3.8h.2020-02-11-3
Space: 55780
Status: successful
Version: 36.3.8h.2020-02-11-3
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Finished at 2020-04-20T08:32:32Z
Build needed 00:30:36, 55780k disk space