fasta3 →
36.3.8h.2020-02-11-4+b3 →
armhf → 2021-09-30 18:16:27
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testbuildd
+==============================================================================+
| fasta3 36.3.8h.2020-02-11-4+b3 (armhf) Thu, 30 Sep 2021 17:35:18 +0000 |
+==============================================================================+
Package: fasta3
Version: 36.3.8h.2020-02-11-4+b3
Source Version: 36.3.8h.2020-02-11-4
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-bef78cd1-3d0f-49a0-9771-cd346073fe04' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bookworm-staging/main Sources [12.4 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.4 MB]
Fetched 25.8 MB in 29s (890 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| 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 bookworm-staging/main fasta3 36.3.8h.2020-02-11-4 (dsc) [2217 B]
Get:2 http://172.17.0.1/private bookworm-staging/main fasta3 36.3.8h.2020-02-11-4 (tar) [1257 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main fasta3 36.3.8h.2020-02-11-4 (diff) [11.8 kB]
Fetched 1271 kB in 1s (1282 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/fasta3-t2TRAQ/fasta3-36.3.8h.2020-02-11' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/fasta3-t2TRAQ' 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-BVKyKx/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-BVKyKx/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-BVKyKx/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: 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 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: 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-BVKyKx/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-BVKyKx/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-BVKyKx/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-BVKyKx/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-BVKyKx/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (2877 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
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:
netbase
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 21 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-BVKyKx/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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Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12484 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), libsimde-dev
Filtered Build-Depends: debhelper-compat (= 13), libsimde-dev
dpkg-deb: building package 'sbuild-build-depends-fasta3-dummy' in '/<<BUILDDIR>>/resolver-BVKyKx/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-BVKyKx/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-BVKyKx/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-BVKyKx/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-BVKyKx/apt_archive ./ Sources [498 B]
Get:5 copy:/<<BUILDDIR>>/resolver-BVKyKx/apt_archive ./ Packages [577 B]
Fetched 2408 B in 1s (3270 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
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:
netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1
libfile-stripnondeterminism-perl libicu67 libmagic-mgc libmagic1
libpipeline1 libsigsegv2 libsimde-dev libsub-override-perl libtool
libuchardet0 libxml2 m4 man-db po-debconf sensible-utils
Suggested packages:
autoconf-archive gnu-standards autoconf-doc 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 libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1
libfile-stripnondeterminism-perl libicu67 libmagic-mgc libmagic1
libpipeline1 libsigsegv2 libsimde-dev libsub-override-perl libtool
libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-fasta3-dummy
sensible-utils
0 upgraded, 33 newly installed, 0 to remove and 21 not upgraded.
Need to get 17.8 MB of archives.
After this operation, 69.1 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-BVKyKx/apt_archive ./ sbuild-build-depends-fasta3-dummy 0.invalid.0 [868 B]
Get:2 http://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-1 [135 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.0.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-7 [793 kB]
Get:5 http://172.17.0.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:6 http://172.17.0.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:7 http://172.17.0.1/private bookworm-staging/main armhf sensible-utils all 0.0.17 [21.5 kB]
Get:8 http://172.17.0.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:9 http://172.17.0.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:10 http://172.17.0.1/private bookworm-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:11 http://172.17.0.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:12 http://172.17.0.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:13 http://172.17.0.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:14 http://172.17.0.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:15 http://172.17.0.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:16 http://172.17.0.1/private bookworm-staging/main armhf automake all 1:1.16.4-2 [819 kB]
Get:17 http://172.17.0.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:18 http://172.17.0.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.2 [192 kB]
Get:19 http://172.17.0.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:20 http://172.17.0.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:21 http://172.17.0.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:22 http://172.17.0.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:23 http://172.17.0.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB]
Get:24 http://172.17.0.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB]
Get:25 http://172.17.0.1/private bookworm-staging/main armhf libelf1 armhf 0.185-2 [168 kB]
Get:26 http://172.17.0.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:27 http://172.17.0.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:28 http://172.17.0.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:29 http://172.17.0.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:30 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.5.2 [1056 kB]
Get:33 http://172.17.0.1/private bookworm-staging/main armhf libsimde-dev all 0.7.2-4 [259 kB]
debconf: delaying package configuration, since apt-utils is not installed
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update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
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Setting up gettext-base (0.21-4) ...
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Setting up autotools-dev (20180224.1+nmu1) ...
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Setting up gettext (0.21-4) ...
Setting up libtool (2.4.6-15) ...
Setting up m4 (1.4.18-5) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up autoconf (2.71-2) ...
Setting up dh-strip-nondeterminism (1.12.0-1) ...
Setting up dwz (0.14-1) ...
Setting up groff-base (1.22.4-7) ...
Setting up automake (1:1.16.4-2) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up dh-autoreconf (20) ...
Setting up debhelper (13.5.2) ...
Setting up sbuild-build-depends-fasta3-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.32-4+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.37-5+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.3.0-9+rpi1 gcc-10_10.3.0-9+rpi1 libc6-dev_2.32-4+rpi1 libstdc++-10-dev_10.3.0-9+rpi1 libstdc++6_11.2.0-4+rpi1 linux-libc-dev_5.10.46-4+rpi1
Package versions: adduser_3.118 apt_2.3.9 autoconf_2.71-2 automake_1:1.16.4-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12+rpi1 base-passwd_3.5.51 bash_5.1-3 binutils_2.37-5+rpi1 binutils-arm-linux-gnueabihf_2.37-5+rpi1 binutils-common_2.37-5+rpi1 bsdextrautils_2.37.2-1 bsdutils_1:2.37.2-1 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.3.0-9+rpi1 dash_0.5.11+git20210120+802ebd4-1 debconf_1.5.77 debhelper_13.5.2 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.4-1 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.3.0-9+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.3.0-9+rpi1 gcc-10-base_10.3.0-9+rpi1 gcc-11-base_11.2.0-4+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.3.9 libarchive-zip-perl_1.68-1 libasan6_11.2.0-4+rpi1 libassuan0_2.5.5-1 libatomic1_11.2.0-4+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.5-1 libaudit1_1:3.0.5-1 libbinutils_2.37-5+rpi1 libblkid1_2.37.2-1 libbz2-1.0_1.0.8-4 libc-bin_2.32-4+rpi1 libc-dev-bin_2.32-4+rpi1 libc6_2.32-4+rpi1 libc6-dev_2.32-4+rpi1 libcap-ng0_0.7.9-2.2+b1 libcc1-0_11.2.0-4+rpi1 libcom-err2_1.46.4-1 libcrypt-dev_1:4.4.25-2 libcrypt1_1:4.4.25-2 libctf-nobfd0_2.37-5+rpi1 libctf0_2.37-5+rpi1 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.2 libdpkg-perl_1.20.9+rpi1 libelf1_0.185-2 libext2fs2_1.46.4-1 libfakeroot_1.25.3-1.1 libffi7_3.3-6 libfile-stripnondeterminism-perl_1.12.0-1 libgcc-10-dev_10.3.0-9+rpi1 libgcc-s1_11.2.0-4+rpi1 libgcrypt20_1.9.4-3 libgdbm-compat4_1.21-1 libgdbm6_1.21-1 libgmp10_2:6.2.1+dfsg-2 libgnutls30_3.7.2-2 libgomp1_11.2.0-4+rpi1 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libhogweed6_3.7.3-1 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.23-1 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libksba8_1.6.0-2 libldap-2.4-2_2.4.59+dfsg-1 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.37.2-1 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncursesw6_6.2+20201114-4 libnettle8_3.7.3-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-2 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-5 libpipeline1_1.5.3-1 libreadline8_8.1-2 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsimde-dev_0.7.2-4 libsmartcols1_2.37.2-1 libsqlite3-0_3.36.0-2 libss2_1.46.4-1 libssl1.1_1.1.1l-1 libstdc++-10-dev_10.3.0-9+rpi1 libstdc++6_11.2.0-4+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.9-1+rpi1 libtasn1-6_4.17.0-2 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.2+20201114-4 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libubsan1_11.2.0-4+rpi1 libuchardet0_0.0.7-1 libudev1_247.9-1+rpi1 libunistring2_0.9.10-6 libuuid1_2.37.2-1 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-2.1+rpi1 linux-libc-dev_5.10.46-4+rpi1 login_1:4.8.1-1 logsave_1.46.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 mount_2.37.2-1 ncurses-base_6.2+20201114-4 ncurses-bin_6.2+20201114-4 netbase_6.3 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-5 perl-base_5.32.1-5 perl-modules-5.32_5.32.1-5 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-fasta3-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021a-1 util-linux_2.37.2-1 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.vlNStV89/trustedkeys.kbx': General error
gpgv: Signature made Thu Sep 9 07:45:51 2021 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./fasta3_36.3.8h.2020-02-11-4.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.2020-02-11-4.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 disc space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 36.3.8h.2020-02-11-4+b3
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-bef78cd1-3d0f-49a0-9771-cd346073fe04
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package fasta3
dpkg-buildpackage: info: source version 36.3.8h.2020-02-11-4+b3
dpkg-buildpackage: info: source distribution bookworm-staging
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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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
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 -g -O2 -ffile-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
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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 -ffile-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
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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 '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':
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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: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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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
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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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
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 -ffile-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 -ffile-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 -ffile-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
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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
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 -ffile-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 -ffile-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
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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
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
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 -ffile-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 -ffile-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 -ffile-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
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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
initfa.c: In function 'alloc_pam2p':
initfa.c:2001:39: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
2001 | "Cannot reallocate pam2p[0]: %ld\n", (nsq+1)*len*sizeof(int));
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long int unsigned int
| %d
dropfz3.c: In function '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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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
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
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}
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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: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 -ffile-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
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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 -ffile-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
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
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 -ffile-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
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 -ffile-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 -ffile-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
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 -ffile-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 -ffile-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 -ffile-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 -ffile-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
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
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 -DNORMAL_DIST -g -O2 -ffile-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
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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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
cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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
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 -ffile-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
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);
| ^
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,
| ^
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: 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
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
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
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
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 'build_ares_code' at build_ares.c:217:4:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
build_ares.c: In function 'build_ares_code':
build_ares.c:217:59: note: length computed here
217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2);
| ^
In function 'strncpy',
inlined from 'build_ares_code' at build_ares.c:217:4:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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 'add_annot_def' at doinit.c:627:7:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
doinit.c: In function 'add_annot_def':
doinit.c:627:7: note: length computed here
627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1));
| ^
In function 'strncpy',
inlined from 'add_annot_def' at doinit.c:627:7:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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,
inlined from 'main' at comp_lib9.c:576:3:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
comp_lib9.c: In function 'main':
doinit.c:991:4: note: length computed here
991 | strncpy(this_opt->s_param,s_param,strlen(s_param));
| ^
In function 'strncpy',
inlined from 'pre_parse_markx' at doinit.c:785:5,
inlined from 'initenv' at doinit.c:402:4,
inlined from 'main' at comp_lib9.c:576:3:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
comp_lib9.c: In function 'main':
doinit.c:785:5: note: length computed here
785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1));
| ^
In function 'strncpy',
inlined from 'set_opt_disp_defs' at doinit.c:991:4,
inlined from 'f_init_opts' at initfa.c:476:3,
inlined from 'f_initenv' at initfa.c:985:3,
inlined from 'initenv' at doinit.c:359:4,
inlined from 'main' at comp_lib9.c:576:3:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
comp_lib9.c: In function 'main':
doinit.c:991:4: note: length computed here
991 | strncpy(this_opt->s_param,s_param,strlen(s_param));
| ^
In function 'strncpy',
inlined from 'pre_parse_markx' at doinit.c:785:5,
inlined from 'initenv' at doinit.c:402:4,
inlined from 'main' at comp_lib9.c:576:3:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
comp_lib9.c: In function 'main':
doinit.c:785:5: note: length computed here
785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1));
| ^
In function 'strncpy',
inlined from 'set_opt_disp_defs' at doinit.c:991:4,
inlined from 'f_init_opts' at initfa.c:476:3,
inlined from 'f_initenv' at initfa.c:985:3,
inlined from 'initenv' at doinit.c:359:4,
inlined from 'main' at comp_lib9.c:576:3:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
comp_lib9.c: In function 'main':
doinit.c:991:4: note: length computed here
991 | strncpy(this_opt->s_param,s_param,strlen(s_param));
| ^
In function 'strncpy',
inlined from 'pre_parse_markx' at doinit.c:785:5,
inlined from 'initenv' at doinit.c:402:4,
inlined from 'main' at comp_lib9.c:576:3:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
comp_lib9.c: In function 'main':
doinit.c:785:5: note: length computed here
785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1));
| ^
In function 'strncpy',
inlined from 'set_opt_disp_defs' at doinit.c:991:4,
inlined from 'f_init_opts' at initfa.c:476:3,
inlined from 'f_initenv' at initfa.c:985:3,
inlined from 'initenv' at doinit.c:359:4,
inlined from 'main' at comp_lib9.c:576:3:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
comp_lib9.c: In function 'main':
doinit.c:991:4: note: length computed here
991 | strncpy(this_opt->s_param,s_param,strlen(s_param));
| ^
In function 'strncpy',
inlined from 'pre_parse_markx' at doinit.c:785:5,
inlined from 'initenv' at doinit.c:402:4,
inlined from 'main' at comp_lib9.c:576:3:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
comp_lib9.c: In function 'main':
doinit.c:785:5: note: length computed here
785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1));
| ^
In function 'strncpy',
inlined from 'add_annot_def' at doinit.c:627:7:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
doinit.c: In function 'add_annot_def':
doinit.c:627:7: note: length computed here
627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1));
| ^
In function 'strncpy',
inlined from 'add_annot_def' at doinit.c:627:7:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
doinit.c: In function 'add_annot_def':
doinit.c:627:7: note: length computed here
627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1));
| ^
In function 'strncpy',
inlined from 'alloc_file_name' at nmgetlib.c:2274:5,
inlined from 'open_lib' at nmgetlib.c:390:26:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
nmgetlib.c: In function 'open_lib':
nmgetlib.c:2267:12: note: length computed here
2267 | fn_len = strlen(f_name);
| ^
In function 'strncpy',
inlined from 'add_file' at lib_sel.c:317:5:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
nmgetlib.c: In function 'open_lib':
nmgetlib.c:2267:12: note: length computed here
2267 | fn_len = strlen(f_name);
| ^
In function 'strncpy',
inlined from 'alloc_file_name' at nmgetlib.c:2274:5,
inlined from 'open_lib' at nmgetlib.c:390:26:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
nmgetlib.c: In function 'open_lib':
nmgetlib.c:2267:12: note: length computed here
2267 | fn_len = strlen(f_name);
| ^
In function 'strncpy',
inlined from 'alloc_file_name' at nmgetlib.c:2274:5,
inlined from 'open_lib' at nmgetlib.c:390:26:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
nmgetlib.c: In function 'open_lib':
nmgetlib.c:2267:12: note: length computed here
2267 | fn_len = strlen(f_name);
| ^
In function 'strncpy',
inlined from 'add_file' at lib_sel.c:317:5:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
lib_sel.c: In function 'add_file':
lib_sel.c:311:7: note: length computed here
311 | len=strlen(tname)+1;
| ^
In function 'strncpy',
inlined from 'showalign.constprop' at mshowalign2.c:577:8:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
lib_sel.c: In function 'add_file':
lib_sel.c:311:7: note: length computed here
311 | len=strlen(tname)+1;
| ^
In function 'strncpy',
inlined from 'add_file' at lib_sel.c:317:5:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
compacc2e.c: In function 'next_annot_entry.constprop':
compacc2e.c:2035:2: note: length computed here
2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment));
| ^
In function 'strncpy',
inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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));
| ^
initfa.c: In function 'get_lambda.constprop':
initfa.c:2224:24: warning: argument 1 value '2294967297' exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
2224 | if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) {
| ^
/usr/include/stdlib.h:542:14: note: in a call to allocation function 'calloc' declared here
542 | extern void *calloc (size_t __nmemb, size_t __size)
| ^
In function 'strncpy',
inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
mshowalign2.c: In function 'showalign.constprop':
url_subs.c:61:19: note: length computed here
61 | n_tmp_annot_s = strlen(annot_s)+1;
| ^
In function 'strncpy',
inlined from 'showalign.constprop' at mshowalign2.c:577:8:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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 'build_ares_code.isra' at build_ares.c:217:4:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
build_ares.c: In function 'build_ares_code.isra':
build_ares.c:217:59: note: length computed here
217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2);
| ^
/usr/bin/ld: /tmp/fasts36.g5bXCs.ltrans0.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:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
compacc2e.c: In function 'next_annot_entry.constprop':
compacc2e.c:2035:2: note: length computed here
2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment));
| ^
In function 'strncpy',
inlined from 'showalign.constprop.isra' at mshowalign2.c:577:8:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
mshowalign2.c: In function 'showalign.constprop.isra':
mshowalign2.c:577:8: note: length computed here
577 | SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string));
| ^
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.isra' at mshowalign2.c:761:7:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
mshowalign2.c: In function 'showalign.constprop.isra':
url_subs.c:61:19: note: length computed here
61 | n_tmp_annot_s = strlen(annot_s)+1;
| ^
In function 'strncpy',
inlined from 'add_annot_def' at doinit.c:627:7:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
doinit.c: In function 'add_annot_def':
doinit.c:627:7: note: length computed here
627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1));
| ^
/usr/bin/ld: /tmp/fasta36.VoM7GE.ltrans0.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 'set_opt_disp_defs' at doinit.c:991:4,
inlined from 'f_init_opts' at initfa.c:476:3,
inlined from 'f_initenv' at initfa.c:985:3,
inlined from 'initenv' at doinit.c:359:4,
inlined from 'main' at comp_lib9.c:576:3:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
comp_lib9.c: In function 'main':
doinit.c:991:4: note: length computed here
991 | strncpy(this_opt->s_param,s_param,strlen(s_param));
| ^
In function 'strncpy',
inlined from 'pre_parse_markx' at doinit.c:785:5,
inlined from 'initenv' at doinit.c:402:4,
inlined from 'main' at comp_lib9.c:576:3:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
comp_lib9.c: In function 'main':
doinit.c:785:5: note: length computed here
785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1));
| ^
In function 'strncpy',
inlined from 'build_ares_code.isra' at build_ares.c:217:4:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
build_ares.c: In function 'build_ares_code.isra':
build_ares.c:217:59: note: length computed here
217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2);
| ^
In function 'strncpy',
inlined from 'build_ares_code' at build_ares.c:217:4:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
build_ares.c: In function 'build_ares_code':
build_ares.c:217:59: note: length computed here
217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2);
| ^
/usr/bin/ld: /tmp/ssearch36.ELCshz.ltrans0.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
comp_lib9.c:250:5: warning: type of 'last_calc' does not match original declaration [-Wlto-type-mismatch]
250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn,
| ^
initfa.c:2036:1: note: type mismatch in parameter 6
2036 | last_calc(
| ^
initfa.c:2036:1: note: 'last_calc' was previously declared here
mshowbest.c:82:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch]
82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p,
| ^
compacc2e.c:2178:1: note: type mismatch in parameter 5
2178 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, long offset, int n1, struct annot_str **annot_p,
| ^
compacc2e.c:2178:1: note: 'get_annot' was previously declared here
compacc2e.c:2178:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
comp_lib9.c:287:1: warning: type of 'showalign' does not match original declaration [-Wlto-type-mismatch]
287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn,
| ^
mshowalign2.c:134:6: note: 'showalign' was previously declared here
134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn,
| ^
mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used
/usr/bin/ld: /tmp/lalign36.wA8sst.ltrans0.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 'set_opt_disp_defs' at doinit.c:991:4,
inlined from 'f_init_opts' at initfa.c:476:3,
inlined from 'f_initenv' at initfa.c:985:3,
inlined from 'initenv' at doinit.c:359:4,
inlined from 'main' at comp_lib9.c:576:3:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
comp_lib9.c: In function 'main':
doinit.c:991:4: note: length computed here
991 | strncpy(this_opt->s_param,s_param,strlen(s_param));
| ^
In function 'strncpy',
inlined from 'pre_parse_markx' at doinit.c:785:5,
inlined from 'initenv' at doinit.c:402:4,
inlined from 'main' at comp_lib9.c:576:3:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
comp_lib9.c: In function 'main':
doinit.c:785:5: note: length computed here
785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1));
| ^
In function 'strncpy',
inlined from 'build_ares_code' at build_ares.c:217:4:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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 'add_annot_def' at doinit.c:627:7:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
doinit.c: In function 'add_annot_def':
doinit.c:627:7: note: length computed here
627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1));
| ^
In function 'strncpy',
inlined from 'add_annot_def' at doinit.c:627:7:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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,
inlined from 'main' at comp_lib9.c:576:3:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
comp_lib9.c: In function 'main':
doinit.c:991:4: note: length computed here
991 | strncpy(this_opt->s_param,s_param,strlen(s_param));
| ^
In function 'strncpy',
inlined from 'pre_parse_markx' at doinit.c:785:5,
inlined from 'initenv' at doinit.c:402:4,
inlined from 'main' at comp_lib9.c:576:3:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
comp_lib9.c: In function 'main':
doinit.c:785:5: note: length computed here
785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1));
| ^
In function 'strncpy',
inlined from 'set_opt_disp_defs' at doinit.c:991:4,
inlined from 'f_init_opts' at initfa.c:476:3,
inlined from 'f_initenv' at initfa.c:985:3,
inlined from 'initenv' at doinit.c:359:4,
inlined from 'main' at comp_lib9.c:576:3:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
comp_lib9.c: In function 'main':
doinit.c:991:4: note: length computed here
991 | strncpy(this_opt->s_param,s_param,strlen(s_param));
| ^
In function 'strncpy',
inlined from 'pre_parse_markx' at doinit.c:785:5,
inlined from 'initenv' at doinit.c:402:4,
inlined from 'main' at comp_lib9.c:576:3:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
comp_lib9.c: In function 'main':
doinit.c:785:5: note: length computed here
785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1));
| ^
In function 'strncpy',
inlined from 'add_annot_def' at doinit.c:627:7:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
doinit.c: In function 'add_annot_def':
doinit.c:627:7: note: length computed here
627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1));
| ^
In function 'strncpy',
inlined from 'alloc_file_name' at nmgetlib.c:2274:5,
inlined from 'open_lib' at nmgetlib.c:390:26:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
nmgetlib.c: In function 'open_lib':
nmgetlib.c:2267:12: note: length computed here
2267 | fn_len = strlen(f_name);
| ^
In function 'strncpy',
inlined from 'add_file' at lib_sel.c:317:5:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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 '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:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
nmgetlib.c: In function 'open_lib':
nmgetlib.c:2267:12: note: length computed here
2267 | fn_len = strlen(f_name);
| ^
In function 'strncpy',
inlined from 'alloc_file_name' at nmgetlib.c:2274:5,
inlined from 'open_lib' at nmgetlib.c:390:26:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
nmgetlib.c: In function 'open_lib':
nmgetlib.c:2267:12: note: length computed here
2267 | fn_len = strlen(f_name);
| ^
In function 'strncpy',
inlined from 'add_file' at lib_sel.c:317:5:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
lib_sel.c: In function 'add_file':
lib_sel.c:311:7: note: length computed here
311 | len=strlen(tname)+1;
| ^
In function 'strncpy',
inlined from 'add_file' at lib_sel.c:317:5:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
lib_sel.c: In function 'add_file':
lib_sel.c:311:7: note: length computed here
311 | len=strlen(tname)+1;
| ^
In function 'strncpy',
inlined from 'showalign.constprop.isra' at mshowalign2.c:577:8:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
mshowalign2.c: In function 'showalign.constprop.isra':
mshowalign2.c:577:8: note: length computed here
577 | SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string));
| ^
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.isra' at mshowalign2.c:761:7:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
mshowalign2.c: In function 'showalign.constprop.isra':
url_subs.c:61:19: note: length computed here
61 | n_tmp_annot_s = strlen(annot_s)+1;
| ^
In function 'strncpy',
inlined from 'showalign.constprop' at mshowalign2.c:577:8:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
lib_sel.c: In function 'add_file':
lib_sel.c:311:7: note: length computed here
311 | len=strlen(tname)+1;
| ^
In function 'strncpy',
inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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 'build_ares_code.isra' at build_ares.c:217:4:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
build_ares.c: In function 'build_ares_code.isra':
build_ares.c:217:59: note: length computed here
217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2);
| ^
In function 'strncpy',
inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
compacc2e.c: In function 'next_annot_entry.constprop':
compacc2e.c:2035:2: note: length computed here
2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment));
| ^
/usr/bin/ld: /tmp/fastx36.KaF49n.ltrans0.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:236:1: warning: type of 'process_hist' does not match original declaration [-Wlto-type-mismatch]
236 | process_hist(struct stat_str *sptr, int nstats,
| ^
scaleswt.c:164:1: note: type mismatch in parameter 7
164 | process_hist(struct stat_str *sptr, int nstats,
| ^
scaleswt.c:164:1: note: 'process_hist' was previously declared here
scaleswt.c:164:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
mshowbest.c:82:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch]
82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p,
| ^
compacc2e.c:2178:1: note: type mismatch in parameter 5
2178 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, long offset, int n1, struct annot_str **annot_p,
| ^
compacc2e.c:2178:1: note: 'get_annot' was previously declared here
compacc2e.c:2178:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
comp_lib9.c:287:1: warning: type of 'showalign' does not match original declaration [-Wlto-type-mismatch]
287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn,
| ^
mshowalign2.c:134:6: note: 'showalign' was previously declared here
134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn,
| ^
mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used
In function 'strncpy',
inlined from 'showalign.constprop' at mshowalign2.c:577:8:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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_annot_def' at doinit.c:627:7:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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 'showalign.constprop.isra' at mshowalign2.c:577:8:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
mshowalign2.c: In function 'showalign.constprop.isra':
mshowalign2.c:577:8: note: length computed here
577 | SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string));
| ^
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.isra' at mshowalign2.c:761:7:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
mshowalign2.c: In function 'showalign.constprop.isra':
url_subs.c:61:19: note: length computed here
61 | n_tmp_annot_s = strlen(annot_s)+1;
| ^
In function 'strncpy',
inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
compacc2e.c: In function 'next_annot_entry.constprop':
compacc2e.c:2035:2: note: length computed here
2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment));
| ^
/usr/bin/ld: /tmp/tfastx36.DeL4vk.ltrans0.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: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 'set_opt_disp_defs' at doinit.c:991:4,
inlined from 'f_init_opts' at initfa.c:476:3,
inlined from 'f_initenv' at initfa.c:985:3,
inlined from 'initenv' at doinit.c:359:4,
inlined from 'main' at comp_lib9.c:576:3:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
comp_lib9.c: In function 'main':
doinit.c:991:4: note: length computed here
991 | strncpy(this_opt->s_param,s_param,strlen(s_param));
| ^
In function 'strncpy',
inlined from 'pre_parse_markx' at doinit.c:785:5,
inlined from 'initenv' at doinit.c:402:4,
inlined from 'main' at comp_lib9.c:576:3:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
comp_lib9.c: In function 'main':
doinit.c:785:5: note: length computed here
785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1));
| ^
In function 'strncpy',
inlined from 'build_ares_code.isra' at build_ares.c:217:4:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
build_ares.c: In function 'build_ares_code.isra':
build_ares.c:217:59: note: length computed here
217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2);
| ^
/usr/bin/ld: /tmp/fasty36.YzP6Yc.ltrans0.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
In function 'strncpy',
inlined from 'add_annot_def' at doinit.c:627:7:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
doinit.c: In function 'add_annot_def':
doinit.c:627:7: note: length computed here
627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1));
| ^
compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch]
954 | re_openlib(struct lmf_str *, int outtty);
| ^
nmgetlib.c:503:3: note: type mismatch in parameter 2
503 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty)
| ^
nmgetlib.c:503:3: note: 're_openlib' was previously declared here
nmgetlib.c:503:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used
mshowbest.c:63:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch]
63 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr);
| ^
compacc2e.c:2290:1: note: type mismatch in parameter 2
2290 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) {
| ^
compacc2e.c:2290:1: note: 's_annot_to_aa1a' was previously declared here
compacc2e.c:2290:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
comp_lib9.c: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
/usr/bin/ld: /tmp/tfasty36.al8mn5.ltrans0.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 'set_opt_disp_defs' at doinit.c:991:4,
inlined from 'f_init_opts' at initfa.c:476:3,
inlined from 'f_initenv' at initfa.c:985:3,
inlined from 'initenv' at doinit.c:359:4,
inlined from 'main' at comp_lib9.c:576:3:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
comp_lib9.c: In function 'main':
doinit.c:991:4: note: length computed here
991 | strncpy(this_opt->s_param,s_param,strlen(s_param));
| ^
In function 'strncpy',
inlined from 'pre_parse_markx' at doinit.c:785:5,
inlined from 'initenv' at doinit.c:402:4,
inlined from 'main' at comp_lib9.c:576:3:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
comp_lib9.c: In function 'main':
doinit.c:785:5: note: length computed here
785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1));
| ^
In function 'strncpy',
inlined from 'add_annot_def' at doinit.c:627:7:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
doinit.c: In function 'add_annot_def':
doinit.c:627:7: note: length computed here
627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1));
| ^
In function 'strncpy',
inlined from 'add_annot_def' at doinit.c:627:7:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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,
inlined from 'main' at comp_lib9.c:576:3:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
comp_lib9.c: In function 'main':
doinit.c:991:4: note: length computed here
991 | strncpy(this_opt->s_param,s_param,strlen(s_param));
| ^
In function 'strncpy',
inlined from 'pre_parse_markx' at doinit.c:785:5,
inlined from 'initenv' at doinit.c:402:4,
inlined from 'main' at comp_lib9.c:576:3:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
comp_lib9.c: In function 'main':
doinit.c:785:5: note: length computed here
785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1));
| ^
In function 'strncpy',
inlined from '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:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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 'set_opt_disp_defs' at doinit.c:991:4,
inlined from 'f_init_opts' at initfa.c:476:3,
inlined from 'f_initenv' at initfa.c:985:3,
inlined from 'initenv' at doinit.c:359:4,
inlined from 'main' at comp_lib9.c:576:3:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
comp_lib9.c: In function 'main':
doinit.c:991:4: note: length computed here
991 | strncpy(this_opt->s_param,s_param,strlen(s_param));
| ^
In function 'strncpy',
inlined from 'pre_parse_markx' at doinit.c:785:5,
inlined from 'initenv' at doinit.c:402:4,
inlined from 'main' at comp_lib9.c:576:3:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
comp_lib9.c: In function 'main':
doinit.c:785:5: note: length computed here
785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1));
| ^
In function 'strncpy',
inlined from 'add_file' at lib_sel.c:317:5:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
nmgetlib.c: In function 'open_lib':
nmgetlib.c:2267:12: note: length computed here
2267 | fn_len = strlen(f_name);
| ^
In function 'strncpy',
inlined from 'showalign.constprop' at mshowalign2.c:577:8:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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 '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:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
nmgetlib.c: In function 'open_lib':
nmgetlib.c:2267:12: note: length computed here
2267 | fn_len = strlen(f_name);
| ^
In function 'strncpy',
inlined from 'add_file' at lib_sel.c:317:5:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
lib_sel.c: In function 'add_file':
lib_sel.c:311:7: note: length computed here
311 | len=strlen(tname)+1;
| ^
In function 'strncpy',
inlined from 'add_file' at lib_sel.c:317:5:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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 'build_ares_code.isra' at build_ares.c:217:4:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
build_ares.c: In function 'build_ares_code.isra':
build_ares.c:217:59: note: length computed here
217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2);
| ^
/usr/bin/ld: /tmp/tfasts36.XDTI4k.ltrans0.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:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
compacc2e.c: In function 'next_annot_entry.constprop':
compacc2e.c:2035:2: note: length computed here
2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment));
| ^
In function 'strncpy',
inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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_annot_def' at doinit.c:627:7:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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 'showalign.constprop.isra' at mshowalign2.c:577:8:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
mshowalign2.c: In function 'showalign.constprop.isra':
mshowalign2.c:577:8: note: length computed here
577 | SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string));
| ^
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.isra' at mshowalign2.c:761:7:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
mshowalign2.c: In function 'showalign.constprop.isra':
url_subs.c:61:19: note: length computed here
61 | n_tmp_annot_s = strlen(annot_s)+1;
| ^
In function 'strncpy',
inlined from 'build_ares_code.isra' at build_ares.c:217:4:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
build_ares.c: In function 'build_ares_code.isra':
build_ares.c:217:59: note: length computed here
217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2);
| ^
/usr/bin/ld: /tmp/fastm36.DQ1LDh.ltrans0.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: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:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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 'set_opt_disp_defs' at doinit.c:991:4,
inlined from 'f_init_opts' at initfa.c:476:3,
inlined from 'f_initenv' at initfa.c:985:3,
inlined from 'initenv' at doinit.c:359:4,
inlined from 'main' at comp_lib9.c:576:3:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
comp_lib9.c: In function 'main':
doinit.c:991:4: note: length computed here
991 | strncpy(this_opt->s_param,s_param,strlen(s_param));
| ^
In function 'strncpy',
inlined from 'pre_parse_markx' at doinit.c:785:5,
inlined from 'initenv' at doinit.c:402:4,
inlined from 'main' at comp_lib9.c:576:3:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
comp_lib9.c: In function 'main':
doinit.c:785:5: note: length computed here
785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1));
| ^
In function 'strncpy',
inlined from 'build_ares_code' at build_ares.c:217:4:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
build_ares.c: In function 'build_ares_code':
build_ares.c:217:59: note: length computed here
217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2);
| ^
In function 'strncpy',
inlined from 'build_ares_code.isra' at build_ares.c:217:4:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
build_ares.c: In function 'build_ares_code.isra':
build_ares.c:217:59: note: length computed here
217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2);
| ^
In function 'strncpy',
inlined from 'build_ares_code.isra' at build_ares.c:217:4:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
build_ares.c: In function 'build_ares_code.isra':
build_ares.c:217:59: note: length computed here
217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2);
| ^
/usr/bin/ld: /tmp/tfastm36.6edxTZ.ltrans0.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:250:5: warning: type of 'last_calc' does not match original declaration [-Wlto-type-mismatch]
250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn,
| ^
initfa.c:2036:1: note: type mismatch in parameter 6
2036 | last_calc(
| ^
initfa.c:2036:1: note: 'last_calc' was previously declared here
mshowbest.c:82:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch]
82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p,
| ^
compacc2e.c:2178:1: note: type mismatch in parameter 5
2178 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, long offset, int n1, struct annot_str **annot_p,
| ^
compacc2e.c:2178:1: note: 'get_annot' was previously declared here
compacc2e.c:2178:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
comp_lib9.c:287:1: warning: type of 'showalign' does not match original declaration [-Wlto-type-mismatch]
287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn,
| ^
mshowalign2.c:134:6: note: 'showalign' was previously declared here
134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn,
| ^
mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used
/usr/bin/ld: /tmp/fastf36.hVumKH.ltrans0.ltrans.o: in function `main':
/<<PKGBUILDDIR>>/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
In function 'strncpy',
inlined from 'set_opt_disp_defs' at doinit.c:991:4,
inlined from 'f_init_opts' at initfa.c:476:3,
inlined from 'f_initenv' at initfa.c:985:3,
inlined from 'initenv' at doinit.c:359:4,
inlined from 'main' at comp_lib9.c:576:3:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
comp_lib9.c: In function 'main':
doinit.c:991:4: note: length computed here
991 | strncpy(this_opt->s_param,s_param,strlen(s_param));
| ^
In function 'strncpy',
inlined from 'pre_parse_markx' at doinit.c:785:5,
inlined from 'initenv' at doinit.c:402:4,
inlined from 'main' at comp_lib9.c:576:3:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
comp_lib9.c: In function 'main':
doinit.c:785:5: note: length computed here
785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1));
| ^
In function 'strncpy',
inlined from 'build_ares_code' at build_ares.c:217:4:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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,
inlined from 'main' at comp_lib9.c:576:3:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
comp_lib9.c: In function 'main':
doinit.c:991:4: note: length computed here
991 | strncpy(this_opt->s_param,s_param,strlen(s_param));
| ^
In function 'strncpy',
inlined from 'pre_parse_markx' at doinit.c:785:5,
inlined from 'initenv' at doinit.c:402:4,
inlined from 'main' at comp_lib9.c:576:3:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
comp_lib9.c: In function 'main':
doinit.c:785:5: note: length computed here
785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1));
| ^
In function 'strncpy',
inlined from '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:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
doinit.c: In function 'add_annot_def':
doinit.c:627:7: note: length computed here
627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1));
| ^
In function 'strncpy',
inlined from 'add_file' at lib_sel.c:317:5:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
lib_sel.c: In function 'add_file':
lib_sel.c:311:7: note: length computed here
311 | len=strlen(tname)+1;
| ^
In function 'strncpy',
inlined from 'add_annot_def' at doinit.c:627:7:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
compacc2e.c: In function 'next_annot_entry.constprop':
compacc2e.c:2035:2: note: length computed here
2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment));
| ^
In function 'strncpy',
inlined from 'showalign.constprop.isra' at mshowalign2.c:577:8:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
mshowalign2.c: In function 'showalign.constprop.isra':
mshowalign2.c:577:8: note: length computed here
577 | SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string));
| ^
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.isra' at mshowalign2.c:761:7:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
mshowalign2.c: In function 'showalign.constprop.isra':
url_subs.c:61:19: note: length computed here
61 | n_tmp_annot_s = strlen(annot_s)+1;
| ^
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:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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 'build_ares_code.isra' at build_ares.c:217:4:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
build_ares.c: In function 'build_ares_code.isra':
build_ares.c:217:59: note: length computed here
217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2);
| ^
In function 'strncpy',
inlined from '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:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
nmgetlib.c: In function 'open_lib':
nmgetlib.c:2267:12: note: length computed here
2267 | fn_len = strlen(f_name);
| ^
In function 'strncpy',
inlined from 'add_file' at lib_sel.c:317:5:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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;
| ^
/usr/bin/ld: /tmp/tfastf36.1u4VRp.ltrans0.ltrans.o: in function `main':
/<<PKGBUILDDIR>>/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
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 'add_file' at lib_sel.c:317:5:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
lib_sel.c: In function 'add_file':
lib_sel.c:311:7: note: length computed here
311 | len=strlen(tname)+1;
| ^
In function 'strncpy',
inlined from 'showalign.constprop' at mshowalign2.c:577:8:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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;
| ^
initfa.c: In function 'get_lambda.constprop':
initfa.c:2224:24: warning: argument 1 value '2294967297' exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
2224 | if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) {
| ^
/usr/include/stdlib.h:542:14: note: in a call to allocation function 'calloc' declared here
542 | extern void *calloc (size_t __nmemb, size_t __size)
| ^
In function 'strncpy',
inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | 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 'next_annot_entry.constprop' at compacc2e.c:2035:2:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^
compacc2e.c: In function 'next_annot_entry.constprop':
compacc2e.c:2035:2: note: length computed here
2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment));
| ^
/usr/bin/ld: /tmp/glsearch36.PRgDgA.ltrans0.ltrans.o: in function `main':
/<<PKGBUILDDIR>>/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
/usr/bin/ld: /tmp/ggsearch36.IuXpiq.ltrans0.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 Thu Sep 30 17:50:33 UTC 2021 on testbuildd
Linux testbuildd 4.9.0-0.bpo.6-armmp #1 SMP Debian 4.9.82-1+deb9u3~bpo8+1 (2018-03-22) armv7l GNU/Linux
starting prss36(ssearch/fastx) Thu Sep 30 17:50:33 UTC 2021
done
starting lalign36 Thu Sep 30 17:50:35 UTC 2021
FINISHED Thu Sep 30 18:02:44 UTC 2021
STARTING FASTA36 Thu Sep 30 18:02:44 UTC 2021 on testbuildd
Linux testbuildd 4.9.0-0.bpo.6-armmp #1 SMP Debian 4.9.82-1+deb9u3~bpo8+1 (2018-03-22) armv7l GNU/Linux
starting prss36(ssearch/fastx) Thu Sep 30 18:02:44 UTC 2021
done
starting lalign36 Thu Sep 30 18:02:46 UTC 2021
FINISHED Thu Sep 30 18:15:06 UTC 2021
# ../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 [486]) MLE statistics: Lambda= 0.1586; K=0.004068
statistics sampled from 4 (4) to 486 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: 0.060
The best scores are: opt bits E(12)
sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu ( 218) 1242 293.9 1.9e-83
sp|P00502|GSTA1_RAT Glutathione S-transferase alph ( 222) 237 64.0 3.2e-14
sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Ho ( 142) 51 21.4 0.13
sp|P00517|KAPCA_BOVIN cAMP-dependent protein kinas ( 351) 43 19.6 1.1
sp|P14960|RBS_GUITH Ribulose bisphosphate carboxyl ( 139) 36 18.0 1.3
sp|P01593|KV101_HUMAN Ig kappa chain V-I region AG ( 108) 31 16.8 2.2
sp|P99998|CYC_PANTR Cytochrome c OS=Pan troglodyte ( 105) 30 16.6 2.4
sp|P02585|TNNC2_HUMAN Troponin C, skeletal muscle ( 160) 30 16.6 3.5
sp|P60615|NXL1A_BUNMU Alpha-bungarotoxin isoform A ( 95) 26 15.7 3.9
sp|P03435|HEMA_I75A3 Hemagglutinin OS=Influenza A ( 567) 37 18.2 4
sp|P00193|FER_PEPAS Ferredoxin OS=Peptostreptococc ( 54) 22 14.8 4.1
sp|P01834|IGKC_HUMAN Ig kappa chain C region OS=Ho ( 106) 23 15.0 6
>>sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu 1 O (218 aa)
initn: 1242 init1: 1242 opt: 1242 Z-score: 1550.0 bits: 293.9 E(12): 1.9e-83
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: 307.1 bits: 64.0 E(12): 3.2e-14
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: 80.6 bits: 21.4 E(12): 0.13
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: 63.7 bits: 19.6 E(12): 1.1
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: 62.3 bits: 18.0 E(12): 1.3
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: 58.0 bits: 16.8 E(12): 2.2
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: 57.0 bits: 16.6 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: 53.7 bits: 16.6 E(12): 3.5
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|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): 3.9
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|P03435|HEMA_I75A3 Hemagglutinin OS=Influenza A viru (567 aa)
initn: 37 init1: 37 opt: 37 Z-score: 52.5 bits: 18.2 E(12): 4
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|P00193|FER_PEPAS Ferredoxin OS=Peptostreptococcus a (54 aa)
initn: 22 init1: 22 opt: 22 Z-score: 52.3 bits: 14.8 E(12): 4.1
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: 48.3 bits: 15.0 E(12): 6
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: Thu Sep 30 18:15:06 2021 done: Thu Sep 30 18:15:06 2021
Total Scan time: 0.060 Total Display time: 0.040
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_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/tfastf36 debian/fasta3/usr/bin/map_db debian/fasta3/usr/bin/fastm36 debian/fasta3/usr/bin/tfastm36 debian/fasta3/usr/bin/tfasts36 debian/fasta3/usr/bin/lalign36 debian/fasta3/usr/bin/fasta36 debian/fasta3/usr/bin/fastx36 debian/fasta3/usr/bin/fastf36 debian/fasta3/usr/bin/tfasty36 debian/fasta3/usr/bin/glsearch36 debian/fasta3/usr/bin/fasty36 debian/fasta3/usr/bin/fasts36 debian/fasta3/usr/bin/tfastx36 debian/fasta3/usr/bin/ssearch36 debian/fasta3/usr/bin/ggsearch36 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-dbgsym' in '../fasta3-dbgsym_36.3.8h.2020-02-11-4+b3_armhf.deb'.
dpkg-deb: building package 'fasta3' in '../fasta3_36.3.8h.2020-02-11-4+b3_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../fasta3_36.3.8h.2020-02-11-4+b3_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 2021-09-30T18:16:19Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
fasta3_36.3.8h.2020-02-11-4+b3_armhf.changes:
---------------------------------------------
Format: 1.8
Date: Thu, 09 Sep 2021 09:29:56 +0200
Source: fasta3 (36.3.8h.2020-02-11-4)
Binary: fasta3 fasta3-dbgsym
Binary-Only: yes
Architecture: armhf
Version: 36.3.8h.2020-02-11-4+b3
Distribution: bookworm-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Raspbian wandboard test autobuilder <root@raspbian.org>
Description:
fasta3 - tools for searching collections of biological sequences
Changes:
fasta3 (36.3.8h.2020-02-11-4+b3) bookworm-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
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fasta3-dbgsym_36.3.8h.2020-02-11-4+b3_armhf.deb
-----------------------------------------------
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lrwxrwxrwx root/root 0 2021-09-09 07:29 ./usr/share/doc/fasta3-dbgsym -> fasta3
fasta3_36.3.8h.2020-02-11-4+b3_armhf.deb
----------------------------------------
new Debian package, version 2.0.
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2193 bytes, 54 lines control
13616 bytes, 184 lines md5sums
Package: fasta3
Source: fasta3 (36.3.8h.2020-02-11-4)
Version: 36.3.8h.2020-02-11-4+b3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5558
Depends: libc6 (>= 2.29), python3
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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| Summary |
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Build Architecture: armhf
Build-Space: 54204
Build-Time: 2165
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 242
Job: fasta3_36.3.8h.2020-02-11-4
Machine Architecture: armhf
Package: fasta3
Package-Time: 2461
Source-Version: 36.3.8h.2020-02-11-4
Space: 54204
Status: successful
Version: 36.3.8h.2020-02-11-4+b3
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Finished at 2021-09-30T18:16:19Z
Build needed 00:41:01, 54204k disc space