kma →
1.3.5-1 →
armhf → 2020-10-20 07:36:55
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| kma 1.3.5-1 (armhf) Tue, 20 Oct 2020 07:31:10 +0000 |
+==============================================================================+
Package: kma
Version: 1.3.5-1
Source Version: 1.3.5-1
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-5178a8b4-7a15-4483-87ee-f711e508b4ad' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.7 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.7 MB]
Fetched 24.4 MB in 24s (1023 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: 'kma' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/kam.git
Please use:
git clone https://salsa.debian.org/med-team/kam.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 747 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main kma 1.3.5-1 (dsc) [1934 B]
Get:2 http://172.17.0.1/private bullseye-staging/main kma 1.3.5-1 (tar) [740 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main kma 1.3.5-1 (diff) [5248 B]
Fetched 747 kB in 0s (3115 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/kma-djNLT3/kma-1.3.5' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/kma-djNLT3' 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-1lfSaj/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-1lfSaj/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-1lfSaj/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-1lfSaj/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-1lfSaj/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-1lfSaj/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-1lfSaj/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-1lfSaj/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (2840 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 packages were automatically installed and are no longer required:
bsdextrautils netbase sensible-utils
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 45 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-1lfSaj/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (22.3 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12514 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)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), zlib1g-dev
Filtered Build-Depends: debhelper-compat (= 13), zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-kma-dummy' in '/<<BUILDDIR>>/resolver-1lfSaj/apt_archive/sbuild-build-depends-kma-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-kma-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-1lfSaj/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-1lfSaj/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-1lfSaj/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-1lfSaj/apt_archive ./ Sources [496 B]
Get:5 copy:/<<BUILDDIR>>/resolver-1lfSaj/apt_archive ./ Packages [574 B]
Fetched 2403 B in 1s (3209 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install kma 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 debhelper dh-autoreconf
dh-strip-nondeterminism dwz file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libcroco3 libdebhelper-perl libelf1
libfile-stripnondeterminism-perl libglib2.0-0 libicu67 libmagic-mgc
libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0
libxml2 m4 man-db po-debconf zlib1g-dev
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 libglib2.0-data shared-mime-info
xdg-user-dirs libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev debhelper dh-autoreconf
dh-strip-nondeterminism dwz file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libcroco3 libdebhelper-perl libelf1
libfile-stripnondeterminism-perl libglib2.0-0 libicu67 libmagic-mgc
libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0
libxml2 m4 man-db po-debconf sbuild-build-depends-kma-dummy zlib1g-dev
0 upgraded, 33 newly installed, 0 to remove and 45 not upgraded.
Need to get 18.6 MB of archives.
After this operation, 68.6 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-1lfSaj/apt_archive ./ sbuild-build-depends-kma-dummy 0.invalid.0 [864 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-4 [801 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.2.1 [188 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.181-1 [161 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.66.1-1 [1174 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-4 [8289 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.1 [578 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.2.1 [1007 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up libicu67:armhf (67.1-4) ...
Setting up libmagic-mgc (1:5.38-5) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.66.1-1) ...
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Setting up libmagic1:armhf (1:5.38-5) ...
Setting up gettext-base (0.19.8.1-10) ...
Setting up file (1:5.38-5) ...
Setting up autotools-dev (20180224.1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libelf1:armhf (0.181-1) ...
Setting up libxml2:armhf (2.9.10+dfsg-6.1) ...
Setting up libfile-stripnondeterminism-perl (1.9.0-1) ...
Setting up libtool (2.4.6-14) ...
Setting up m4 (1.4.18-4) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up autoconf (2.69-11.1) ...
Setting up dh-strip-nondeterminism (1.9.0-1) ...
Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-5) ...
Setting up automake (1:1.16.2-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up gettext (0.19.8.1-10) ...
Setting up man-db (2.9.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up po-debconf (1.0.21) ...
Setting up dh-autoreconf (19) ...
Setting up debhelper (13.2.1) ...
Setting up sbuild-build-depends-kma-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-3+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.35-2+rpi1 dpkg-dev_1.20.5+rpi1 g++-10_10.2.0-5+rpi1 gcc-10_10.2.0-5+rpi1 libc6-dev_2.31-3+rpi1 libstdc++-10-dev_10.2.0-5+rpi1 libstdc++6_10.2.0-5+rpi1 linux-libc-dev_5.7.10-1+rpi1
Package versions: adduser_3.118 apt_2.1.10 aptitude_0.8.13-2 aptitude-common_0.8.13-2 autoconf_2.69-11.1 automake_1:1.16.2-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-7 binutils_2.35-2+rpi1 binutils-arm-linux-gnueabihf_2.35-2+rpi1 binutils-common_2.35-2+rpi1 bsdextrautils_2.36-3 bsdutils_1:2.36-3 build-essential_12.8 bzip2_1.0.8-4 coreutils_8.30-3 cpp_4:10.1.0-1+rpi1 cpp-10_10.2.0-5+rpi1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2.1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.20.5+rpi1 dpkg-dev_1.20.5+rpi1 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.36-3 file_1:5.38-5 findutils_4.7.0-1 g++_4:10.1.0-1+rpi1 g++-10_10.2.0-5+rpi1 gcc_4:10.1.0-1+rpi1 gcc-10_10.2.0-5+rpi1 gcc-10-base_10.2.0-5+rpi1 gcc-6-base_6.5.0-1+rpi3 gcc-7-base_7.5.0-6+rpi1+b1 gcc-8-base_8.4.0-4+rpi1+b1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libapt-pkg6.0_2.1.10 libarchive-zip-perl_1.68-1 libasan6_10.2.0-5+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.0-5+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libbinutils_2.35-2+rpi1 libblkid1_2.36-3 libboost-iostreams1.71.0_1.71.0-6+b1 libbz2-1.0_1.0.8-4 libc-bin_2.31-3+rpi1 libc-dev-bin_2.31-3+rpi1 libc6_2.31-3+rpi1 libc6-dev_2.31-3+rpi1 libcap-ng0_0.7.9-2.2 libcc1-0_10.2.0-5+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35-2+rpi1 libctf0_2.35-2+rpi1 libcwidget4_0.5.18-5 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.253 libdebhelper-perl_13.2.1 libdpkg-perl_1.20.5+rpi1 libelf1_0.181-1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.36-3 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-10-dev_10.2.0-5+rpi1 libgcc-s1_10.2.0-5+rpi1 libgcrypt20_1.8.6-2 libgdbm-compat4_1.18.1-5.1 libgdbm6_1.18.1-5.1 libglib2.0-0_2.66.1-1 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.14-2+b1 libgomp1_10.2.0-5+rpi1 libgpg-error0_1.38-2 libhogweed6_3.6-2 libicu67_67.1-4 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libksba8_1.4.0-2 libldap-2.4-2_2.4.51+dfsg-1 libldap-common_2.4.51+dfsg-1 liblocale-gettext-perl_1.07-4 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.36-3 libmpc3_1.2.0~rc1-1 libmpfr6_4.1.0-3 libncursesw6_6.2-1 libnettle8_3.6-2 libnpth0_1.6-2 libp11-kit0_0.23.21-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.30_5.30.3-4 libpipeline1_1.5.3-1 libreadline8_8.0-4 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+rpi1 libselinux1_3.1-2 libsemanage-common_3.1-1 libsemanage1_3.1-1 libsepol1_3.1-1 libsigc++-2.0-0v5_2.10.2-1 libsigsegv2_2.12-2 libsmartcols1_2.36-3 libsqlite3-0_3.33.0-1 libss2_1.45.6-1 libstdc++-10-dev_10.2.0-5+rpi1 libstdc++6_10.2.0-5+rpi1 libsub-override-perl_0.09-2 libsystemd0_246.2-1+rpi1 libtasn1-6_4.16.0-2 libtext-charwidth-perl_0.04-10 libtext-iconv-perl_1.7-7 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10.2.0-5+rpi1 libuchardet0_0.0.7-1 libudev1_246.2-1+rpi1 libunistring2_0.9.10-4 libuuid1_2.36-3 libxapian30_1.4.17-1 libxml2_2.9.10+dfsg-6.1 libzstd1_1.4.5+dfsg-4+rpi1 linux-libc-dev_5.7.10-1+rpi1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.36-3 ncurses-base_6.2-1 ncurses-bin_6.2-1 netbase_6.1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-4 po-debconf_1.0.21 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-kma-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-4 tar_1.30+dfsg-7 tzdata_2020a-1 util-linux_2.36-3 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.XSiKi0Qy/trustedkeys.kbx': General error
gpgv: Signature made Sun Oct 18 06:38:51 2020 UTC
gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
gpgv: issuer "npatra974@gmail.com"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./kma_1.3.5-1.dsc
dpkg-source: info: extracting kma in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking kma_1.3.5.orig.tar.bz2
dpkg-source: info: unpacking kma_1.3.5-1.debian.tar.xz
Check disc space
----------------
Sufficient free space for build
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=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-5178a8b4-7a15-4483-87ee-f711e508b4ad
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package kma
dpkg-buildpackage: info: source version 1.3.5-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
dh_auto_clean
make -j4 clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -f align.o alnfrags.o ankers.o assembly.o chain.o compdna.o compkmers.o compress.o db.o decon.o dist.o ef.o filebuff.o frags.o hashmap.o hashmapcci.o hashmapkma.o hashmapkmers.o hashtable.o index.o kma.o kmapipe.o kmeranker.o kmers.o kmmap.o loadupdate.o makeindex.o matrix.o mt1.o nw.o pherror.o printconsensus.o qseqs.o qualcheck.o runinput.o runkma.o sam.o savekmers.o seq2fasta.o seqmenttree.o seqparse.o shm.o sparse.o spltdb.o stdnuc.o stdstat.o tmp.o update.o updateindex.o updatescores.o valueshash.o vcf.o xml.o kma kma_index kma_shm kma_update libkma.a
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
dh_auto_build -a
make -j4 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o align.o align.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o alnfrags.o alnfrags.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ankers.o ankers.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o assembly.o assembly.c
In file included from align.c:28:
align.c: In function 'KMA':
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
align.c:91:55: note: in expansion of macro 'getNuc'
91 | for(j = i - 1; 0 <= j && 0 <= prev && qseq[j] == getNuc(template_index->seq, prev); --j) {
| ^~~~~~
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
align.c:104:51: note: in expansion of macro 'getNuc'
104 | while(i < end && value < t_len && qseq[i] == getNuc(template_index->seq, value)) {
| ^~~~~~
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
align.c:144:56: note: in expansion of macro 'getNuc'
144 | for(j = k - 1; 0 <= j && 0 <= prev && qseq[j] == getNuc(template_index->seq, prev); --j) {
| ^~~~~~
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
align.c:157:52: note: in expansion of macro 'getNuc'
157 | while(k < end && value < t_len && qseq[k] == getNuc(template_index->seq, value)) {
| ^~~~~~
align.c: In function 'KMA_score':
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
align.c:467:55: note: in expansion of macro 'getNuc'
467 | for(k = j - 1; 0 <= k && 0 <= prev && qseq[k] == getNuc(template_index->seq, prev); --k) {
| ^~~~~~
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
align.c:482:51: note: in expansion of macro 'getNuc'
482 | while(j < end && value < t_len && qseq[j] == getNuc(template_index->seq, value)) {
| ^~~~~~
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
align.c:512:56: note: in expansion of macro 'getNuc'
512 | for(k = l - 1; 0 <= k && 0 <= prev && qseq[k] == getNuc(template_index->seq, prev); --k) {
| ^~~~~~
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
align.c:526:52: note: in expansion of macro 'getNuc'
526 | while(l < end && value < t_len && qseq[l] == getNuc(template_index->seq, value)) {
| ^~~~~~
ankers.c: In function 'get_ankers':
ankers.c:202:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
202 | fread(qseq->seq, sizeof(long unsigned), qseq->complen, inputfile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ankers.c:203:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
203 | fread(qseq->N + 1, sizeof(int), qseq->N[0], inputfile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ankers.c:204:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
204 | fread(out_Tem + 1, sizeof(int), *out_Tem, inputfile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ankers.c:205:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
205 | fread(header->seq, 1, header->len, inputfile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
align.c: In function 'anker_rc':
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
align.c:817:55: note: in expansion of macro 'getNuc'
817 | for(j = i - 1; 0 <= j && 0 <= prev && qseq[j] == getNuc(template_index->seq, prev); --j) {
| ^~~~~~
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
align.c:832:51: note: in expansion of macro 'getNuc'
832 | while(i < end && value < t_len && qseq[i] == getNuc(template_index->seq, value)) {
| ^~~~~~
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
align.c:875:56: note: in expansion of macro 'getNuc'
875 | for(j = k - 1; 0 <= j && 0 <= prev && qseq[j] == getNuc(template_index->seq, prev); --j) {
| ^~~~~~
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
align.c:888:52: note: in expansion of macro 'getNuc'
888 | while(k < end && value < t_len && qseq[k] == getNuc(template_index->seq, value)) {
| ^~~~~~
align.c: In function 'anker_rc_comp':
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
align.c:1007:55: note: in expansion of macro 'getNuc'
1007 | for(j = i - 1; 0 <= j && 0 <= prev && qseq[j] == getNuc(template_index->seq, prev); --j) {
| ^~~~~~
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
align.c:1022:51: note: in expansion of macro 'getNuc'
1022 | while(i < end && value < t_len && qseq[i] == getNuc(template_index->seq, value)) {
| ^~~~~~
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
align.c:1058:56: note: in expansion of macro 'getNuc'
1058 | for(j = k - 1; 0 <= j && 0 <= prev && qseq[j] == getNuc(template_index->seq, prev); --j) {
| ^~~~~~
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
align.c:1071:52: note: in expansion of macro 'getNuc'
1071 | while(k < end && value < t_len && qseq[k] == getNuc(template_index->seq, value)) {
| ^~~~~~
In file included from assembly.c:38:
assembly.c: In function 'updateMatrix':
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
assembly.c:121:72: note: in expansion of macro 'getNuc'
121 | check = sprintf(update, "%c\t%hu\t%hu\t%hu\t%hu\t%hu\t%hu\n", bases[getNuc(template_seq, i)], assembly[pos].counts[0], assembly[pos].counts[1], assembly[pos].counts[2], assembly[pos].counts[3], assembly[pos].counts[4], assembly[pos].counts[5]);
| ^~~~~~
assembly.c: In function 'assemble_KMA_threaded':
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
assembly.c:686:32: note: in expansion of macro 'getNuc'
686 | aligned_assem->t[i] = bases[getNuc(template_index->seq, pos)];
| ^~~~~~
assembly.c: In function 'assemble_KMA_dense_threaded':
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
assembly.c:858:26: note: in expansion of macro 'getNuc'
858 | aligned_assem->t[i] = getNuc(template_index->seq, i);
| ^~~~~~
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
assembly.c:1124:13: note: in expansion of macro 'getNuc'
1124 | bestNuc = getNuc(template_index->seq, i);
| ^~~~~~
assembly.c: In function 'callConsensus':
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
assembly.c:1476:34: note: in expansion of macro 'getNuc'
1476 | aligned_assem->t[i] = bases[getNuc(seq, pos)];
| ^~~~~~
assembly.c: In function 'assemble_KMA_threaded':
assembly.c:370:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
370 | fread(buffer, sizeof(int), 8, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assembly.c:391:6: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
391 | fread(qseq->seq, 1, qseq->len, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assembly.c:392:6: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
392 | fread(header->seq, 1, header->len, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assembly.c: In function 'assemble_KMA_dense_threaded':
assembly.c:915:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
915 | fread(buffer, sizeof(int), 8, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assembly.c:942:6: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
942 | fread(qseq->seq, 1, qseq->len, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assembly.c:943:6: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
943 | fread(header->seq, 1, header->len, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assembly.c: In function 'skip_assemble_KMA':
assembly.c:1238:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1238 | fread(buffer, sizeof(int), 8, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assembly.c:1258:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1258 | fread(qseq->seq, 1, qseq->len, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assembly.c:1259:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1259 | fread(header->seq, 1, header->len, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assembly.c: In function 'assemble_KMA':
assembly.c:1794:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1794 | fread(buffer, sizeof(int), 8, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assembly.c:1815:6: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1815 | fread(qseq->seq, 1, qseq->len, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assembly.c:1816:6: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1816 | fread(header->seq, 1, header->len, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o chain.o chain.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o compdna.o compdna.c
In file included from compdna.c:25:
compdna.c: In function 'unCompDNA':
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
compdna.c:187:12: note: in expansion of macro 'getNuc'
187 | *--seq = getNuc(compressor->seq, i);
| ^~~~~~
compdna.c: In function 'binRev':
compdna.c:225:15: warning: right shift count >= width of type [-Wshift-count-overflow]
225 | return ((mer >> 32) | (mer << 32));
| ^~
compdna.c:225:29: warning: left shift count >= width of type [-Wshift-count-overflow]
225 | return ((mer >> 32) | (mer << 32));
| ^~
compdna.c: In function 'getComp':
compdna.c:322:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
322 | fread(&compressor->seqlen, sizeof(int), 1, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o compkmers.o compkmers.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o compress.o compress.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o db.o db.c
compress.c: In function 'compressKMA_DB':
compress.c:105:8: warning: right shift count >= width of type [-Wshift-count-overflow]
105 | check >>= 32;
| ^~~
compress.c: In function 'compressKMA_deconDB':
compress.c:941:9: warning: right shift count >= width of type [-Wshift-count-overflow]
941 | check >>= 32;
| ^~~
compress.c: In function 'compressKMA_deconMegaDB':
compress.c:1044:9: warning: right shift count >= width of type [-Wshift-count-overflow]
1044 | check >>= 32;
| ^~~
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o decon.o decon.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dist.o dist.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ef.o ef.c
In file included from ef.c:25:
ef.c: In function 'getExtendedFeatures':
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
ef.c:95:52: note: in expansion of macro 'getNuc'
95 | snpSum += (depthUpdate - assembly[pos].counts[getNuc(seq, pos)]);
| ^~~~~~
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filebuff.o filebuff.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o frags.o frags.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashmap.o hashmap.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashmapcci.o hashmapcci.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashmapkma.o hashmapkma.c
hashmapcci.c: In function 'hashMapCCI_initialize':
hashmapcci.c:54:15: warning: right shift count >= width of type [-Wshift-count-overflow]
54 | size |= size >> 32;
| ^~
hashmapcci.c: In function 'hashMapCCI_load':
hashmapcci.c:472:2: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
472 | read(seq, src->seq, ((src->len >> 5) + 1) * sizeof(long unsigned));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hashmapcci.c: In function 'hashMapCCI_load_thread':
hashmapcci.c:499:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
499 | read(seq, src->seq, ((src->len >> 5) + 1) * sizeof(long unsigned));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashmapkmers.o hashmapkmers.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashtable.o hashtable.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o index.o index.c
index.c: In function 'index_main':
index.c:340:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
340 | fread(inputfiles[filecount - 1], 1, size - 1, inputfile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
index.c:390:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
390 | fread(deconfiles[deconcount - 1], 1, size - 1, inputfile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kma.o kma.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmapipe.o kmapipe.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmeranker.o kmeranker.c
kma.c: In function 'kma_main':
kma.c:1158:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1158 | fread(&qseq.len, sizeof(int), 1, templatefile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kma.c:1153:34: warning: argument 1 null where non-null expected [-Wnonnull]
1153 | myTemplatefilename = smalloc(strlen(templatefilename) + 64);
| ^~~~~~~~~~~~~~~~~~~~~~~~
In file included from kma.c:22:
/usr/include/string.h:385:15: note: in a call to function 'strlen' declared here
385 | extern size_t strlen (const char *__s)
| ^~~~~~
kma.c:1199:32: warning: argument 1 null where non-null expected [-Wnonnull]
1199 | myTemplatefilename = smalloc(strlen(templatefilename) + 64);
| ^~~~~~~~~~~~~~~~~~~~~~~~
In file included from kma.c:22:
/usr/include/string.h:385:15: note: in a call to function 'strlen' declared here
385 | extern size_t strlen (const char *__s)
| ^~~~~~
kma.c:1205:32: warning: argument 1 null where non-null expected [-Wnonnull]
1205 | myTemplatefilename = smalloc(strlen(templatefilename) + 64);
| ^~~~~~~~~~~~~~~~~~~~~~~~
In file included from kma.c:22:
/usr/include/string.h:385:15: note: in a call to function 'strlen' declared here
385 | extern size_t strlen (const char *__s)
| ^~~~~~
kma.c:1217:32: warning: argument 1 null where non-null expected [-Wnonnull]
1217 | myTemplatefilename = smalloc(strlen(templatefilename) + 64);
| ^~~~~~~~~~~~~~~~~~~~~~~~
In file included from kma.c:22:
/usr/include/string.h:385:15: note: in a call to function 'strlen' declared here
385 | extern size_t strlen (const char *__s)
| ^~~~~~
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmers.o kmers.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmmap.o kmmap.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loadupdate.o loadupdate.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o makeindex.o makeindex.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o matrix.o matrix.c
loadupdate.c: In function 'load_DBs':
loadupdate.c:175:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
175 | fread(&DB_size, sizeof(unsigned), 1, infile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
loadupdate.c:180:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
180 | fread(*template_lengths, sizeof(unsigned), DB_size, infile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
loadupdate.c:181:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
181 | fread(*template_slengths, sizeof(unsigned), DB_size, infile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
loadupdate.c:182:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
182 | fread(*template_ulengths, sizeof(unsigned), DB_size, infile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
loadupdate.c:190:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
190 | fread(*template_lengths, sizeof(unsigned), DB_size, infile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mt1.o mt1.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o nw.o nw.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o pherror.o pherror.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o printconsensus.o printconsensus.c
mt1.c: In function 'runKMA_Mt1':
mt1.c:183:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
183 | fread(&DB_size, sizeof(int), 1, DB_file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from nw.c:24:
nw.c: In function 'NW':
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
nw.c:73:21: note: in expansion of macro 'getNuc'
73 | aligned->t[m] = getNuc(template, nuc_pos);
| ^~~~~~
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
nw.c:160:11: note: in expansion of macro 'getNuc'
160 | t_nuc = getNuc(template, nuc_pos);
| ^~~~~~
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
nw.c:257:27: note: in expansion of macro 'getNuc'
257 | aligned->t[Stat.len] = getNuc(template, nuc_pos);
| ^~~~~~
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
nw.c:265:28: note: in expansion of macro 'getNuc'
265 | aligned->t[Stat.len] = getNuc(template, nuc_pos);
| ^~~~~~
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
nw.c:272:27: note: in expansion of macro 'getNuc'
272 | aligned->t[Stat.len] = getNuc(template, nuc_pos);
| ^~~~~~
nw.c: In function 'NW_band':
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
nw.c:348:21: note: in expansion of macro 'getNuc'
348 | aligned->t[m] = getNuc(template, nuc_pos);
| ^~~~~~
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
nw.c:449:11: note: in expansion of macro 'getNuc'
449 | t_nuc = getNuc(template, nuc_pos);
| ^~~~~~
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
nw.c:576:27: note: in expansion of macro 'getNuc'
576 | aligned->t[Stat.len] = getNuc(template, nuc_pos);
| ^~~~~~
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
nw.c:584:28: note: in expansion of macro 'getNuc'
584 | aligned->t[Stat.len] = getNuc(template, nuc_pos);
| ^~~~~~
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
nw.c:592:27: note: in expansion of macro 'getNuc'
592 | aligned->t[Stat.len] = getNuc(template, nuc_pos);
| ^~~~~~
nw.c: In function 'NW_score':
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
nw.c:739:11: note: in expansion of macro 'getNuc'
739 | t_nuc = getNuc(template, nuc_pos);
| ^~~~~~
nw.c: In function 'NW_band_score':
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
nw.c:993:11: note: in expansion of macro 'getNuc'
993 | t_nuc = getNuc(template, nuc_pos);
| ^~~~~~
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o qseqs.o qseqs.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o qualcheck.o qualcheck.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o runinput.o runinput.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o runkma.o runkma.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
runkma.c: In function 'runKMA':
runkma.c:581:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
581 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:582:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
582 | fread(header->seq, 1, header->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:583:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
583 | fread(best_start_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:584:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
584 | fread(best_end_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:585:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
585 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:680:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
680 | fread(stats, sizeof(int), 3, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:684:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
684 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:685:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
685 | fread(header->seq, 1, header->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:729:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
729 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:782:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
782 | fread(stats, sizeof(int), 2, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:825:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
825 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:849:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
849 | fread(stats, sizeof(int), 2, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:865:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
865 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:866:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
866 | fread(header->seq, 1, header->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:867:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
867 | fread(best_start_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:868:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
868 | fread(best_end_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:869:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
869 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1015:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1015 | fread(stats, sizeof(int), 3, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1019:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1019 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1020:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1020 | fread(header->seq, 1, header->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c: In function 'runKMA_MEM':
runkma.c:1668:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1668 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1669:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1669 | fread(header->seq, 1, header->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1670:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1670 | fread(best_start_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1671:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1671 | fread(best_end_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1672:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1672 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1767:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1767 | fread(stats, sizeof(int), 3, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1771:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1771 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1772:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1772 | fread(header->seq, 1, header->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1816:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1816 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1869:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1869 | fread(stats, sizeof(int), 2, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1912:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1912 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1936:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1936 | fread(stats, sizeof(int), 2, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1952:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1952 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1953:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1953 | fread(header->seq, 1, header->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1954:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1954 | fread(best_start_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1955:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1955 | fread(best_end_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1956:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1956 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:2099:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
2099 | fread(stats, sizeof(int), 3, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:2103:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
2103 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:2104:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
2104 | fread(header->seq, 1, header->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o savekmers.o savekmers.c
savekmers.c: In function 'loadFsa':
savekmers.c:83:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
83 | fread(qseq->seq, sizeof(long unsigned), qseq->complen, inputfile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
savekmers.c:84:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
84 | fread(qseq->N + 1, sizeof(int), qseq->N[0], inputfile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
savekmers.c:85:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
85 | fread(header->seq, 1, header->len, inputfile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seq2fasta.o seq2fasta.c
In file included from seq2fasta.c:28:
seq2fasta.c: In function 'printFastas':
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
seq2fasta.c:89:19: note: in expansion of macro 'getNuc'
89 | *--seq = bases[getNuc(compseq, j)];
| ^~~~~~
seq2fasta.c: In function 'printFastaList':
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
seq2fasta.c:151:20: note: in expansion of macro 'getNuc'
151 | *--seq = bases[getNuc(compseq, j)];
| ^~~~~~
seq2fasta.c: In function 'printFastas':
seq2fasta.c:84:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
84 | fread(compseq, sizeof(long unsigned), (template_lengths[i] >> 5) + 1, seqfile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
seq2fasta.c: In function 'printFastaList':
seq2fasta.c:146:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
146 | fread(compseq, sizeof(long unsigned), (template_lengths[i] >> 5) + 1, seqfile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seqmenttree.o seqmenttree.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seqparse.o seqparse.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o shm.o shm.c
shm.c: In function 'hashMapKMA_setupSHM':
shm.c:95:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
95 | fread(dest->exist, 1, size, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
shm.c:115:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
115 | fread(dest->values, 1, size, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
shm.c:138:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
138 | fread(dest->key_index, 1, size, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
shm.c:158:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
158 | fread(dest->value_index, 1, size, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
shm.c: In function 'length_setupSHM':
shm.c:263:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
263 | fread(template_lengths, sizeof(unsigned), size / sizeof(unsigned), file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
shm.c: In function 'seq_setupSHM':
shm.c:305:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
305 | fread(seq, sizeof(long unsigned), size / sizeof(long unsigned), file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
shm.c: In function 'name_setupSHM':
shm.c:347:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
347 | fread(template_names, 1, size, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sparse.o sparse.c
sparse.c: In function 'load_DBs_Sparse':
sparse.c:156:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
156 | fread(*template_lengths, sizeof(int), DB_size, DB_file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sparse.c:157:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
157 | fread(*template_ulengths, sizeof(int), DB_size, DB_file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sparse.c:197:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
197 | fread(template_names[0], 1, file_size, DB_file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o spltdb.o spltdb.c
spltdb.c: In function 'runKMA_spltDB':
spltdb.c:461:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
461 | fread(template_lengths + dbBiases[i], sizeof(int), bias, inputfile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:880:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
880 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:881:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
881 | fread(header->seq, 1, header->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:882:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
882 | fread(best_start_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:883:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
883 | fread(best_end_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:884:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
884 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:979:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
979 | fread(stats, sizeof(int), 3, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:983:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
983 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:984:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
984 | fread(header->seq, 1, header->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1028:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1028 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1081:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1081 | fread(stats, sizeof(int), 2, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1124:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1124 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1148:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1148 | fread(stats, sizeof(int), 2, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1164:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1164 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1165:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1165 | fread(header->seq, 1, header->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1166:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1166 | fread(best_start_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1167:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1167 | fread(best_end_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1168:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1168 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1312:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1312 | fread(stats, sizeof(int), 3, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1316:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1316 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1317:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1317 | fread(header->seq, 1, header->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stdnuc.o stdnuc.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stdstat.o stdstat.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tmp.o tmp.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o update.o update.c
update.c: In function 'convertLength_014to015':
update.c:40:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
40 | fread(&size, sizeof(unsigned), 1, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
update.c: In function 'hashMapKMA_014to015':
update.c:88:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
88 | fread(&DB_size, sizeof(unsigned), 1, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
update.c:89:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
89 | fread(&dest->kmersize, sizeof(unsigned), 1, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
update.c:90:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
90 | fread(&dest->prefix_len, sizeof(unsigned), 1, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
update.c:91:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
91 | fread(&dest->prefix, sizeof(long unsigned), 1, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
update.c:92:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
92 | fread(&dest->size, sizeof(long unsigned), 1, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
update.c:100:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
100 | fread(&tmp, sizeof(unsigned), 1, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
update.c:102:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
102 | fread(&seqsize, sizeof(unsigned), 1, file); //seq size
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
update.c:103:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
103 | fread(&tmp, sizeof(unsigned), 1, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
update.c:105:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
105 | fread(&tmp, sizeof(unsigned), 1, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o updateindex.o updateindex.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o updatescores.o updatescores.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o valueshash.o valueshash.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c
In file included from vcf.c:26:
vcf.c: In function 'updateVcf':
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
| ^~
vcf.c:123:16: note: in expansion of macro 'getNuc'
123 | nuc = bases[getNuc(template_seq, pos)];
| ^~~~~~
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o xml.o xml.c
ar -csru libkma.a align.o alnfrags.o ankers.o assembly.o chain.o compdna.o compkmers.o compress.o db.o decon.o dist.o ef.o filebuff.o frags.o hashmap.o hashmapcci.o hashmapkma.o hashmapkmers.o hashtable.o index.o kma.o kmapipe.o kmeranker.o kmers.o kmmap.o loadupdate.o makeindex.o matrix.o mt1.o nw.o pherror.o printconsensus.o qseqs.o qualcheck.o runinput.o runkma.o sam.o savekmers.o seq2fasta.o seqmenttree.o seqparse.o shm.o sparse.o spltdb.o stdnuc.o stdstat.o tmp.o update.o updateindex.o updatescores.o valueshash.o vcf.o xml.o
ar: `u' modifier ignored since `D' is the default (see `U')
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -o kma main.c libkma.a -lm -lpthread -lz -Wl,-z,relro -Wl,-z,now
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -o kma_index kma_index.c libkma.a -lm -lz -Wl,-z,relro -Wl,-z,now
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -o kma_shm kma_shm.c libkma.a -Wl,-z,relro -Wl,-z,now
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -o kma_update kma_update.c libkma.a -Wl,-z,relro -Wl,-z,now
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
create-stamp debian/debhelper-build-stamp
dh_testroot -a
dh_prep -a
dh_auto_install -a
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_dwz -a -a
dwz: debian/kma/usr/bin/kma: DWARF compression not beneficial - old size 270956 new size 274340
dh_strip -a -a
dh_makeshlibs -a -a
dh_shlibdeps -a -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/kma/usr/bin/kma debian/kma/usr/bin/kma_shm were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'kma' in '../kma_1.3.5-1_armhf.deb'.
dpkg-deb: building package 'kma-dbgsym' in '../kma-dbgsym_1.3.5-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../kma_1.3.5-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2020-10-20T07:36:37Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
kma_1.3.5-1_armhf.changes:
--------------------------
Format: 1.8
Date: Sun, 18 Oct 2020 11:46:53 +0530
Source: kma
Binary: kma kma-dbgsym
Architecture: armhf
Version: 1.3.5-1
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Nilesh Patra <npatra974@gmail.com>
Description:
kma - mapping genomic sequences to raw reads directly against redundant
Changes:
kma (1.3.5-1) unstable; urgency=medium
.
* Team upload.
* New upstream version
Checksums-Sha1:
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d0903a6911b8c76c418ec67be31df0832f9fa5b9 4482 kma_1.3.5-1_armhf.buildinfo
6d9be47443e03befba34b2da72877774175f904c 112116 kma_1.3.5-1_armhf.deb
Checksums-Sha256:
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53f89a8c25375cab77ef5450c9b5b4130d4ff08406a148025ebd39c9e935126c 4482 kma_1.3.5-1_armhf.buildinfo
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Files:
495d0828f4a0c8aeb3d05f97eb9ffde8 388148 debug optional kma-dbgsym_1.3.5-1_armhf.deb
efea818882ccb4a2abfd62cf4f49efc7 4482 science optional kma_1.3.5-1_armhf.buildinfo
a2c6a7aca3a20631e92fce4a7c64bf9b 112116 science optional kma_1.3.5-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
kma-dbgsym_1.3.5-1_armhf.deb
----------------------------
new Debian package, version 2.0.
size 388148 bytes: control archive=692 bytes.
436 bytes, 12 lines control
401 bytes, 4 lines md5sums
Package: kma-dbgsym
Source: kma
Version: 1.3.5-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 425
Depends: kma (= 1.3.5-1)
Section: debug
Priority: optional
Description: debug symbols for kma
Build-Ids: 1244275c7b2a8239eaa49d1bb1f384fd04ae9459 b3c4a5cee1dee2cf466832108a1147e7149b137b df8e7af48ffcb78e723bac18d01e87ea54570c7f
drwxr-xr-x root/root 0 2020-10-18 06:16 ./
drwxr-xr-x root/root 0 2020-10-18 06:16 ./usr/
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lrwxrwxrwx root/root 0 2020-10-18 06:16 ./usr/share/doc/kma-dbgsym -> kma
kma_1.3.5-1_armhf.deb
---------------------
new Debian package, version 2.0.
size 112116 bytes: control archive=1068 bytes.
882 bytes, 17 lines control
543 bytes, 9 lines md5sums
Package: kma
Version: 1.3.5-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 300
Depends: libc6 (>= 2.29), zlib1g (>= 1:1.1.4)
Section: science
Priority: optional
Homepage: https://bitbucket.org/genomicepidemiology/kma
Description: mapping genomic sequences to raw reads directly against redundant databases
KMA is mapping a method designed to map raw reads directly against
redundant databases, in an ultra-fast manner using seed and extend. KMA
is particularly good at aligning high quality reads against highly
redundant databases, where unique matches often does not exist. It works
for long low quality reads as well, such as those from Nanopore. Non-
unique matches are resolved using the "ConClave" sorting scheme, and a
consensus sequence are outputtet in addition to other common attributes.
drwxr-xr-x root/root 0 2020-10-18 06:16 ./
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drwxr-xr-x root/root 0 2020-10-18 06:16 ./usr/bin/
-rwxr-xr-x root/root 267976 2020-10-18 06:16 ./usr/bin/kma
-rwxr-xr-x root/root 5668 2020-10-18 06:16 ./usr/bin/kma_index
-rwxr-xr-x root/root 13912 2020-10-18 06:16 ./usr/bin/kma_shm
drwxr-xr-x root/root 0 2020-10-18 06:16 ./usr/share/
drwxr-xr-x root/root 0 2020-10-18 06:16 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-10-18 06:16 ./usr/share/doc/kma/
-rw-r--r-- root/root 2947 2020-10-14 08:53 ./usr/share/doc/kma/README.md.gz
-rw-r--r-- root/root 702 2020-10-18 06:16 ./usr/share/doc/kma/changelog.Debian.gz
-rw-r--r-- root/root 952 2020-10-18 06:16 ./usr/share/doc/kma/copyright
drwxr-xr-x root/root 0 2020-10-18 06:16 ./usr/share/man/
drwxr-xr-x root/root 0 2020-10-18 06:16 ./usr/share/man/man1/
-rw-r--r-- root/root 1312 2020-10-18 06:16 ./usr/share/man/man1/kma.1.gz
-rw-r--r-- root/root 697 2020-10-18 06:16 ./usr/share/man/man1/kma_index.1.gz
-rw-r--r-- root/root 426 2020-10-18 06:16 ./usr/share/man/man1/kma_shm.1.gz
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| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 8656
Build-Time: 94
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 184
Job: kma_1.3.5-1
Machine Architecture: armhf
Package: kma
Package-Time: 327
Source-Version: 1.3.5-1
Space: 8656
Status: successful
Version: 1.3.5-1
--------------------------------------------------------------------------------
Finished at 2020-10-20T07:36:37Z
Build needed 00:05:27, 8656k disc space