kma →
1.2.12-1 →
armhf → 2019-10-28 23:03:35
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testbuildd
+==============================================================================+
| kma 1.2.12-1 (armhf) Mon, 28 Oct 2019 22:54:36 +0000 |
+==============================================================================+
Package: kma
Version: 1.2.12-1
Source Version: 1.2.12-1
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-001b516c-6a33-4c14-9f29-d5049e275dfe' 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 [11.5 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.9 MB]
Fetched 24.4 MB in 30s (809 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 731 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main kma 1.2.12-1 (dsc) [1918 B]
Get:2 http://172.17.0.1/private bullseye-staging/main kma 1.2.12-1 (tar) [724 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main kma 1.2.12-1 (diff) [4964 B]
Fetched 731 kB in 1s (827 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/kma-On2Q6I/kma-1.2.12' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/kma-On2Q6I' 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-hkohaS/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-hkohaS/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-hkohaS/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-hkohaS/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-hkohaS/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-hkohaS/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-hkohaS/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-hkohaS/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2819 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:
libpam-cap netbase
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 7 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-hkohaS/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12235 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 (= 12), zlib1g-dev
Filtered Build-Depends: debhelper-compat (= 12), zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-kma-dummy' in '/<<BUILDDIR>>/resolver-hkohaS/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-hkohaS/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-hkohaS/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-hkohaS/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-hkohaS/apt_archive ./ Sources [496 B]
Get:5 copy:/<<BUILDDIR>>/resolver-hkohaS/apt_archive ./ Packages [576 B]
Fetched 2405 B in 1s (3196 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 packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3
libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libglib2.0-0
libicu63 libmagic-mgc libmagic1 libncurses6 libpipeline1 libsigsegv2
libsub-override-perl libtinfo5 libtool libuchardet0 libxml2 m4 man-db
po-debconf sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less
www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libgpm2 libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3
libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libglib2.0-0
libicu63 libmagic-mgc libmagic1 libncurses6 libpipeline1 libsigsegv2
libsub-override-perl libtinfo5 libtool libuchardet0 libxml2 m4 man-db
po-debconf sbuild-build-depends-kma-dummy sensible-utils zlib1g-dev
0 upgraded, 38 newly installed, 0 to remove and 7 not upgraded.
Need to get 18.9 MB of archives.
After this operation, 67.7 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-hkohaS/apt_archive ./ sbuild-build-depends-kma-dummy 0.invalid.0 [860 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.1+20190803-1 [314 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-3 [782 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.1-2 [26.6 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.0-1 [1261 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12 [15.8 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.37-6 [253 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.37-6 [111 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.37-6 [66.2 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-2 [185 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-11 [547 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.67-1 [104 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.6.1-1 [23.5 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.6.1-1 [14.4 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-1 [69.7 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 12.7.1 [173 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.62.2-1 [1135 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+b2 [571 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.1+20190803-1 [79.3 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.7.1 [997 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking libbsd0:armhf (0.10.0-1) ...
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Setting up libpipeline1:armhf (1.5.1-2) ...
Setting up libmagic-mgc (1:5.37-6) ...
Setting up libarchive-zip-perl (1.67-1) ...
Setting up libglib2.0-0:armhf (2.62.2-1) ...
No schema files found: doing nothing.
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Setting up libmagic1:armhf (1:5.37-6) ...
Setting up gettext-base (0.19.8.1-9) ...
Setting up file (1:5.37-6) ...
Setting up libicu63:armhf (63.2-2) ...
Setting up autotools-dev (20180224.1) ...
Setting up libncurses6:armhf (6.1+20190803-1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up autopoint (0.19.8.1-9) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up sensible-utils (0.0.12) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libtinfo5:armhf (6.1+20190803-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-7+b2) ...
Setting up libfile-stripnondeterminism-perl (1.6.1-1) ...
Setting up libtool (2.4.6-11) ...
Setting up m4 (1.4.18-2) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up autoconf (2.69-11) ...
Setting up dwz (0.13-1) ...
Setting up groff-base (1.22.4-3) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up gettext (0.19.8.1-9) ...
Setting up man-db (2.9.0-1) ...
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 debhelper (12.7.1) ...
Setting up dh-autoreconf (19) ...
Setting up dh-strip-nondeterminism (1.6.1-1) ...
Setting up sbuild-build-depends-kma-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.29-2+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_2.32.51.20190909-1+rpi1 dpkg-dev_1.19.7 g++-9_9.2.1-8+rpi1 gcc-9_9.2.1-8+rpi1 libc6-dev_2.29-2+rpi1 libstdc++-9-dev_9.2.1-8+rpi1 libstdc++6_9.2.1-8+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.46 bash_5.0-4 binutils_2.32.51.20190909-1+rpi1 binutils-arm-linux-gnueabihf_2.32.51.20190909-1+rpi1 binutils-common_2.32.51.20190909-1+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3 cpp_4:9.2.1-3+rpi1 cpp-9_9.2.1-8+rpi1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.7.1 debianutils_4.9 dh-autoreconf_19 dh-strip-nondeterminism_1.6.1-1 diffutils_1:3.7-3 dirmngr_2.2.17-3+b1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-1 e2fsprogs_1.45.4-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.37-6 findutils_4.7.0-1 g++_4:9.2.1-3+rpi1 g++-9_9.2.1-8+rpi1 gcc_4:9.2.1-3+rpi1 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-6-base_6.5.0-1+rpi1+b3 gcc-7-base_7.4.0-14 gcc-9_9.2.1-8+rpi1 gcc-9-base_9.2.1-8+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gnupg_2.2.17-3 gnupg-l10n_2.2.17-3 gnupg-utils_2.2.17-3+b1 gpg_2.2.17-3+b1 gpg-agent_2.2.17-3+b1 gpg-wks-client_2.2.17-3+b1 gpg-wks-server_2.2.17-3+b1 gpgconf_2.2.17-3+b1 gpgsm_2.2.17-3+b1 gpgv_2.2.17-3+b1 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3 hostname_3.22 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-2 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-8+rpi1 libassuan0_2.5.3-7 libatomic1_9.2.1-8+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2 libbinutils_2.32.51.20190909-1+rpi1 libblkid1_2.34-0.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-2+rpi1 libc-dev-bin_2.29-2+rpi1 libc6_2.29-2+rpi1 libc6-dev_2.29-2+rpi1 libcap-ng0_0.7.9-2 libcap2_1:2.25-2 libcap2-bin_1:2.25-2 libcc1-0_9.2.1-8+rpi1 libcom-err2_1.45.4-1 libcroco3_0.6.13-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.249 libdebhelper-perl_12.7.1 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libext2fs2_1.45.4-1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.6.1-1 libgcc-9-dev_9.2.1-8+rpi1 libgcc1_1:9.2.1-8+rpi1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.62.2-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.9-5 libgomp1_9.2.1-8+rpi1 libgpg-error0_1.36-7 libhogweed4_3.4.1-1 libicu63_63.2-2 libidn2-0_2.2.0-2 libisl19_0.20-2 libisl21_0.21-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.48+dfsg-1+b1 libldap-common_2.4.48+dfsg-1 liblz4-1_1.9.1-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-6 libmagic1_1:5.37-6 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncurses6_6.1+20190803-1 libncursesw6_6.1+20190803-1 libnettle6_3.4.1-1 libnpth0_1.6-1 libp11-kit0_0.23.17-2 libpam-cap_1:2.25-2 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_10.32-5 libpcre3_2:8.39-12 libperl5.30_5.30.0-7 libpipeline1_1.5.1-2 libreadline7_7.0-5 libreadline8_8.0-3 libsasl2-2_2.1.27+dfsg-1+b1 libsasl2-modules-db_2.1.27+dfsg-1+b1 libseccomp2_2.4.1-2+rpi1 libselinux1_2.9-2 libsemanage-common_2.9-3 libsemanage1_2.9-3 libsepol1_2.9-2 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.30.1-1 libss2_1.45.4-1 libstdc++-9-dev_9.2.1-8+rpi1 libstdc++6_9.2.1-8+rpi1 libsub-override-perl_0.09-2 libsystemd0_242-7+rpi1 libtasn1-6_4.14-3 libtinfo5_6.1+20190803-1 libtinfo6_6.1+20190803-1 libtool_2.4.6-11 libubsan1_9.2.1-8+rpi1 libuchardet0_0.0.6-3 libudev1_242-7+rpi1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml2_2.9.4+dfsg1-7+b2 libzstd1_1.4.3+dfsg-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.7-2 logsave_1.45.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.9.0-1 mawk_1.3.3-17 mount_2.34-0.1 ncurses-base_6.1+20190803-1 ncurses-bin_6.1+20190803-1 netbase_5.6 passwd_1:4.7-2 patch_2.7.6-6 perl_5.30.0-7 perl-base_5.30.0-7 perl-modules-5.30_5.30.0-7 pinentry-curses_1.1.0-3 po-debconf_1.0.21 raspbian-archive-keyring_20120528.2 readline-common_8.0-3 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 sysvinit-utils_2.96~beta-3 tar_1.30+dfsg-6 tzdata_2019c-3 util-linux_2.34-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Mon Sep 23 08:18:10 2019 UTC
gpgv: using RSA key 84C1977A89E7EFED3E5CA62E2FD8BEDAC020EED1
gpgv: issuer "moeller@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./kma_1.2.12-1.dsc
dpkg-source: info: extracting kma in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking kma_1.2.12.orig.tar.bz2
dpkg-source: info: unpacking kma_1.2.12-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying hardening.patch
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-001b516c-6a33-4c14-9f29-d5049e275dfe
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 1.2.12-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot 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 decon.o ef.o filebuff.o frags.o hashmap.o hashmapindex.o hashmapkma.o hashmapkmers.o hashtable.o index.o kma.o kmapipe.o kmeranker.o kmerlink.o kmers.o kmmap.o loadupdate.o makeindex.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 kma kma_index kma_shm kma_update libkma.a
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
debian/rules build-arch
dh build-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 -Wall -O3 -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 -Wall -O3 -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 -Wall -O3 -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 -Wall -O3 -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:90:55: note: in expansion of macro 'getNuc'
90 | 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:103:51: note: in expansion of macro 'getNuc'
103 | 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:143:56: note: in expansion of macro 'getNuc'
143 | 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:156:52: note: in expansion of macro 'getNuc'
156 | 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:453:54: note: in expansion of macro 'getNuc'
453 | 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:468:50: note: in expansion of macro 'getNuc'
468 | 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:499:55: note: in expansion of macro 'getNuc'
499 | 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:513:51: note: in expansion of macro 'getNuc'
513 | while(l < end && value < t_len && qseq[l] == getNuc(template_index->seq, value)) {
| ^~~~~~
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:781:55: note: in expansion of macro 'getNuc'
781 | 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:796:51: note: in expansion of macro 'getNuc'
796 | 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:839:56: note: in expansion of macro 'getNuc'
839 | 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:852:52: note: in expansion of macro 'getNuc'
852 | while(k < end && value < t_len && qseq[k] == 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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from assembly.c:36:
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:122:72: note: in expansion of macro 'getNuc'
122 | 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:646:32: note: in expansion of macro 'getNuc'
646 | 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:821:26: note: in expansion of macro 'getNuc'
821 | aligned_assem->t[i] = getNuc(template_index->seq, i);
| ^~~~~~
assembly.c: In function 'assemble_KMA_threaded':
assembly.c:388:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
388 | fread(buffer, sizeof(int), 8, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assembly.c:415:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
415 | fread(qseq->seq, 1, qseq->len, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assembly.c:416:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
416 | fread(header->seq, 1, header->len, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assembly.c: In function 'assemble_KMA_dense_threaded':
assembly.c:862:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
862 | fread(buffer, sizeof(int), 8, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assembly.c:889:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
889 | fread(qseq->seq, 1, qseq->len, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assembly.c:890:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
890 | fread(header->seq, 1, header->len, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assembly.c: In function 'skip_assemble_KMA':
assembly.c:1137:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1137 | fread(buffer, sizeof(int), 8, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assembly.c:1157:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1157 | fread(qseq->seq, 1, qseq->len, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assembly.c:1158:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1158 | fread(header->seq, 1, header->len, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -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 -Wall -O3 -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:154:12: note: in expansion of macro 'getNuc'
154 | *--seq = getNuc(compressor->seq, i);
| ^~~~~~
compdna.c: In function 'binRev':
compdna.c:192:15: warning: right shift count >= width of type [-Wshift-count-overflow]
192 | return ((mer >> 32) | (mer << 32));
| ^~
compdna.c:192:29: warning: left shift count >= width of type [-Wshift-count-overflow]
192 | return ((mer >> 32) | (mer << 32));
| ^~
compdna.c: In function 'getComp':
compdna.c:289:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
289 | fread(&compressor->seqlen, sizeof(int), 1, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -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 -Wall -O3 -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 -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o decon.o decon.c
compress.c: In function 'compressKMA_DB':
compress.c:103:8: warning: right shift count >= width of type [-Wshift-count-overflow]
103 | check >>= 32;
| ^~~
compress.c: In function 'compressKMA_deconDB':
compress.c:939:9: warning: right shift count >= width of type [-Wshift-count-overflow]
939 | check >>= 32;
| ^~~
compress.c: In function 'compressKMA_deconMegaDB':
compress.c:1042:9: warning: right shift count >= width of type [-Wshift-count-overflow]
1042 | check >>= 32;
| ^~~
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -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:82:51: note: in expansion of macro 'getNuc'
82 | snpSum += (depthUpdate - assembly[pos].counts[getNuc(template_seq, pos)]);
| ^~~~~~
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -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 -Wall -O3 -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 -Wall -O3 -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 -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashmapindex.o hashmapindex.c
hashmapindex.c: In function 'hashMap_index_load':
hashmapindex.c:267:2: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
267 | read(seq, src->seq, ((src->len >> 5) + 1) * sizeof(long unsigned));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hashmapindex.c:268:2: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
268 | read(index, src->index, src->size * sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hashmapindex.c: In function 'hashMap_index_build':
hashmapindex.c:293:2: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
293 | read(seq, src->seq, ((src->len >> 5) + 1) * sizeof(long unsigned));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hashmapindex.c: In function 'alignLoad_shm_initial':
hashmapindex.c:369:2: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
369 | read(index_in, &kmersize, sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashmapkma.o hashmapkma.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -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 -Wall -O3 -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 -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o index.o index.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kma.o kma.c
index.c: In function 'index_main':
index.c:343:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
343 | fread(inputfiles[filecount - 1], 1, size - 1, inputfile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
index.c:396:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
396 | fread(deconfiles[deconcount - 1], 1, size - 1, inputfile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -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 -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmeranker.o kmeranker.c
kma.c: In function 'kma_main':
kma.c:1093:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1093 | fread(&qseq.len, sizeof(int), 1, templatefile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kma.c:1088:34: warning: argument 1 null where non-null expected [-Wnonnull]
1088 | myTemplatefilename = smalloc(strlen(templatefilename) + 64);
| ^~~~~~~~~~~~~~~~~~~~~~~~
In file included from kma.c:22:
/usr/include/string.h:384:15: note: in a call to function 'strlen' declared here
384 | extern size_t strlen (const char *__s)
| ^~~~~~
kma.c:1132:32: warning: argument 1 null where non-null expected [-Wnonnull]
1132 | myTemplatefilename = smalloc(strlen(templatefilename) + 64);
| ^~~~~~~~~~~~~~~~~~~~~~~~
In file included from kma.c:22:
/usr/include/string.h:384:15: note: in a call to function 'strlen' declared here
384 | extern size_t strlen (const char *__s)
| ^~~~~~
kma.c:1138:32: warning: argument 1 null where non-null expected [-Wnonnull]
1138 | myTemplatefilename = smalloc(strlen(templatefilename) + 64);
| ^~~~~~~~~~~~~~~~~~~~~~~~
In file included from kma.c:22:
/usr/include/string.h:384:15: note: in a call to function 'strlen' declared here
384 | extern size_t strlen (const char *__s)
| ^~~~~~
kma.c:1150:32: warning: argument 1 null where non-null expected [-Wnonnull]
1150 | myTemplatefilename = smalloc(strlen(templatefilename) + 64);
| ^~~~~~~~~~~~~~~~~~~~~~~~
In file included from kma.c:22:
/usr/include/string.h:384:15: note: in a call to function 'strlen' declared here
384 | extern size_t strlen (const char *__s)
| ^~~~~~
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmerlink.o kmerlink.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -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 -Wall -O3 -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 -Wall -O3 -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 -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o makeindex.o makeindex.c
loadupdate.c: In function 'load_DBs':
loadupdate.c:178:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
178 | fread(&DB_size, sizeof(unsigned), 1, infile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
loadupdate.c:183:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
183 | fread(*template_lengths, sizeof(unsigned), DB_size, infile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
loadupdate.c:184:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
184 | fread(*template_slengths, sizeof(unsigned), DB_size, infile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
loadupdate.c:185:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
185 | fread(*template_ulengths, sizeof(unsigned), DB_size, infile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
loadupdate.c:193:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
193 | fread(*template_lengths, sizeof(unsigned), DB_size, infile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mt1.o mt1.c
mt1.c: In function 'runKMA_Mt1':
mt1.c:166:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
166 | fread(&DB_size, sizeof(int), 1, DB_file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -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 -Wall -O3 -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 -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o printconsensus.o printconsensus.c
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:161:11: note: in expansion of macro 'getNuc'
161 | 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:258:27: note: in expansion of macro 'getNuc'
258 | 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:266:28: note: in expansion of macro 'getNuc'
266 | 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:273:27: note: in expansion of macro 'getNuc'
273 | 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:349:21: note: in expansion of macro 'getNuc'
349 | 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:452:11: note: in expansion of macro 'getNuc'
452 | 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:585:27: note: in expansion of macro 'getNuc'
585 | 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:593:28: note: in expansion of macro 'getNuc'
593 | 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:601:27: note: in expansion of macro 'getNuc'
601 | 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:748:11: note: in expansion of macro 'getNuc'
748 | 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:1003:11: note: in expansion of macro 'getNuc'
1003 | t_nuc = getNuc(template, nuc_pos);
| ^~~~~~
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -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 -Wall -O3 -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 -Wall -O3 -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 -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o runkma.o runkma.c
runkma.c: In function 'runKMA':
runkma.c:216:3: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
216 | read(index_in_no, &kmersize, sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:573:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
573 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:574:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
574 | fread(header->seq, 1, header->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:575:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
575 | fread(best_start_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:576:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
576 | fread(best_end_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:577:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
577 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:672:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
672 | fread(stats, sizeof(int), 3, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:676:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
676 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:677:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
677 | fread(header->seq, 1, header->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:721:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
721 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:774:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
774 | fread(stats, sizeof(int), 2, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:817:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
817 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:841:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
841 | fread(stats, sizeof(int), 2, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:857:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
857 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:858:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
858 | fread(header->seq, 1, header->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:859:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
859 | fread(best_start_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:860:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
860 | fread(best_end_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:861:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
861 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1007:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1007 | fread(stats, sizeof(int), 3, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1011:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1011 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1012:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1012 | fread(header->seq, 1, header->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c: In function 'runKMA_MEM':
runkma.c:1346:3: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
1346 | read(index_in_no, &kmersize, sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1591:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1591 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1592:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1592 | fread(header->seq, 1, header->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1593:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1593 | fread(best_start_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1594:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1594 | fread(best_end_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1595:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1595 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1690:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1690 | fread(stats, sizeof(int), 3, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1694:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1694 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1695:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1695 | fread(header->seq, 1, header->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1739:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1739 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1792:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1792 | fread(stats, sizeof(int), 2, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1835:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1835 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1859:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1859 | fread(stats, sizeof(int), 2, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1875:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1875 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1876:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1876 | fread(header->seq, 1, header->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1877:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1877 | fread(best_start_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1878:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1878 | fread(best_end_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1879:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1879 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:2025:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
2025 | fread(stats, sizeof(int), 3, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:2029:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
2029 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:2030:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
2030 | fread(header->seq, 1, header->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o savekmers.o savekmers.c
savekmers.c: In function 'loadFsa':
savekmers.c:84:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
84 | fread(qseq->seq, sizeof(long unsigned), qseq->complen, inputfile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
savekmers.c:85:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
85 | fread(qseq->N + 1, sizeof(int), qseq->N[0], inputfile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
savekmers.c:86:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
86 | fread(header->seq, 1, header->len, inputfile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -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 -Wall -O3 -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 -Wall -O3 -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 -Wall -O3 -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 'index_setupSHM':
shm.c:305:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
305 | fread(index, sizeof(int), size / sizeof(int), file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
shm.c: In function 'seq_setupSHM':
shm.c:346:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
346 | fread(seq, sizeof(long unsigned), size / sizeof(long unsigned), file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
shm.c: In function 'name_setupSHM':
shm.c:388:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
388 | fread(template_names, 1, size, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -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 -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o spltdb.o spltdb.c
spltdb.c: In function 'runKMA_spltDB':
spltdb.c:460:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
460 | fread(template_lengths + dbBiases[i], sizeof(int), bias, inputfile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:849:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
849 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:850:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
850 | fread(header->seq, 1, header->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:851:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
851 | fread(best_start_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:852:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
852 | fread(best_end_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:853:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
853 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:948:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
948 | fread(stats, sizeof(int), 3, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:952:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
952 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:953:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
953 | fread(header->seq, 1, header->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:997:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
997 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1050:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1050 | fread(stats, sizeof(int), 2, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1093:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1093 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1117:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1117 | fread(stats, sizeof(int), 2, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1133:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1133 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1134:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1134 | fread(header->seq, 1, header->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1135:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1135 | fread(best_start_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1136:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1136 | fread(best_end_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1137:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1137 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1281:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1281 | fread(stats, sizeof(int), 3, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1285:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1285 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1286:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1286 | fread(header->seq, 1, header->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1525:3: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
1525 | read(index_in_no, &kmersize, sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1569:5: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
1569 | read(index_in_no, &kmersize, sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -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 -Wall -O3 -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 -Wall -O3 -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 -Wall -O3 -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 -Wall -O3 -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 -Wall -O3 -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 -Wall -O3 -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 -Wall -O3 -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:122:16: note: in expansion of macro 'getNuc'
122 | nuc = bases[getNuc(template_seq, pos)];
| ^~~~~~
ar -csru libkma.a align.o alnfrags.o ankers.o assembly.o chain.o compdna.o compkmers.o compress.o decon.o ef.o filebuff.o frags.o hashmap.o hashmapindex.o hashmapkma.o hashmapkmers.o hashtable.o index.o kma.o kmapipe.o kmeranker.o kmerlink.o kmers.o kmmap.o loadupdate.o makeindex.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
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 -Wall -O3 -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 -Wall -O3 -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 -Wall -O3 -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 -Wall -O3 -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
fakeroot debian/rules binary-arch
dh binary-arch
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
dwz: debian/kma/usr/bin/kma: DWARF compression not beneficial - old size 233180 new size 234510
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/kma/usr/bin/kma_shm debian/kma/usr/bin/kma 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_1.2.12-1_armhf.deb'.
dpkg-deb: building package 'kma-dbgsym' in '../kma-dbgsym_1.2.12-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../kma_1.2.12-1_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 2019-10-28T23:03:29Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
kma_1.2.12-1_armhf.changes:
---------------------------
Format: 1.8
Date: Mon, 23 Sep 2019 09:58:31 +0200
Source: kma
Binary: kma kma-dbgsym
Architecture: armhf
Version: 1.2.12-1
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Steffen Moeller <moeller@debian.org>
Description:
kma - mapping genomic sequences to raw reads directly against redundant
Changes:
kma (1.2.12-1) unstable; urgency=medium
.
* Team upload.
* New upstream version
Checksums-Sha1:
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854dd690d3b878f6ff08adce103e39917d50e9c2 4522 kma_1.2.12-1_armhf.buildinfo
23e137137bc52245b6273589a11a6e3698aa844c 98084 kma_1.2.12-1_armhf.deb
Checksums-Sha256:
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79f58612101c5f035dfadf08a59724e7baf6fa039d67899037390469771bb00a 4522 kma_1.2.12-1_armhf.buildinfo
c5a34fe96d089c26e804982b23d00bf8cd903a6a6c8bc55250b19a92f628340a 98084 kma_1.2.12-1_armhf.deb
Files:
da62001e3d30fb8e0c12a92ba177262d 339616 debug optional kma-dbgsym_1.2.12-1_armhf.deb
2e64676ad025cf6db605b62c3c67e943 4522 science optional kma_1.2.12-1_armhf.buildinfo
2432037e4dd206e7fc5f96a87c298a1b 98084 science optional kma_1.2.12-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
kma-dbgsym_1.2.12-1_armhf.deb
-----------------------------
new Debian package, version 2.0.
size 339616 bytes: control archive=696 bytes.
438 bytes, 12 lines control
401 bytes, 4 lines md5sums
Package: kma-dbgsym
Source: kma
Version: 1.2.12-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 375
Depends: kma (= 1.2.12-1)
Section: debug
Priority: optional
Description: debug symbols for kma
Build-Ids: 6372a49fa93bc6d82bfd70971583a9811ae62504 d48a74039abf9c1c4d1b1cb7cb1cf79547258b7b e54385d8f7973b4cd20fab25d3099c8b65f0015e
drwxr-xr-x root/root 0 2019-09-23 07:58 ./
drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/
drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/lib/
drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/lib/debug/
drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/lib/debug/.build-id/63/
-rw-r--r-- root/root 334772 2019-09-23 07:58 ./usr/lib/debug/.build-id/63/72a49fa93bc6d82bfd70971583a9811ae62504.debug
drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/lib/debug/.build-id/d4/
-rw-r--r-- root/root 21428 2019-09-23 07:58 ./usr/lib/debug/.build-id/d4/8a74039abf9c1c4d1b1cb7cb1cf79547258b7b.debug
drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/lib/debug/.build-id/e5/
-rw-r--r-- root/root 8876 2019-09-23 07:58 ./usr/lib/debug/.build-id/e5/4385d8f7973b4cd20fab25d3099c8b65f0015e.debug
drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 3876 2019-09-23 07:58 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/kma.debug
drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/share/
drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/share/doc/
lrwxrwxrwx root/root 0 2019-09-23 07:58 ./usr/share/doc/kma-dbgsym -> kma
kma_1.2.12-1_armhf.deb
----------------------
new Debian package, version 2.0.
size 98084 bytes: control archive=1068 bytes.
883 bytes, 17 lines control
543 bytes, 9 lines md5sums
Package: kma
Version: 1.2.12-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 260
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 2019-09-23 07:58 ./
drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/
drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/bin/
-rwxr-xr-x root/root 226996 2019-09-23 07:58 ./usr/bin/kma
-rwxr-xr-x root/root 5668 2019-09-23 07:58 ./usr/bin/kma_index
-rwxr-xr-x root/root 13912 2019-09-23 07:58 ./usr/bin/kma_shm
drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/share/
drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/share/doc/
drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/share/doc/kma/
-rw-r--r-- root/root 2989 2019-09-09 07:18 ./usr/share/doc/kma/README.md.gz
-rw-r--r-- root/root 323 2019-09-23 07:58 ./usr/share/doc/kma/changelog.Debian.gz
-rw-r--r-- root/root 952 2019-09-23 07:58 ./usr/share/doc/kma/copyright
drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/share/man/
drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/share/man/man1/
-rw-r--r-- root/root 1312 2019-09-23 07:58 ./usr/share/man/man1/kma.1.gz
-rw-r--r-- root/root 697 2019-09-23 07:58 ./usr/share/man/man1/kma_index.1.gz
-rw-r--r-- root/root 426 2019-09-23 07:58 ./usr/share/man/man1/kma_shm.1.gz
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Build Architecture: armhf
Build-Space: 7880
Build-Time: 81
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 400
Job: kma_1.2.12-1
Machine Architecture: armhf
Package: kma
Package-Time: 533
Source-Version: 1.2.12-1
Space: 7880
Status: successful
Version: 1.2.12-1
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Finished at 2019-10-28T23:03:29Z
Build needed 00:08:53, 7880k disc space