kma →
1.3.2-1 →
armhf → 2020-07-19 05:33:19
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-01
+==============================================================================+
| kma 1.3.2-1 (armhf) Sun, 19 Jul 2020 05:26:10 +0000 |
+==============================================================================+
Package: kma
Version: 1.3.2-1
Source Version: 1.3.2-1
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bullseye-staging-armhf-sbuild-ae703480-aac7-4c93-a776-a97b1f999e8a' 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 [11.8 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.9 MB]
Fetched 24.6 MB in 25s (999 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| 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 746 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main kma 1.3.2-1 (dsc) [1911 B]
Get:2 http://172.17.0.1/private bullseye-staging/main kma 1.3.2-1 (tar) [739 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main kma 1.3.2-1 (diff) [4740 B]
Fetched 746 kB in 0s (6021 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/kma-SdFmVv/kma-1.3.2' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/kma-SdFmVv' 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-0d1atj/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-0d1atj/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-0d1atj/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-0d1atj/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-0d1atj/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-0d1atj/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-0d1atj/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-0d1atj/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-0d1atj/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2667 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-0d1atj/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-0d1atj/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
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 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 4 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-0d1atj/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 (22.3 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12307 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) ...
+------------------------------------------------------------------------------+
| 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-0d1atj/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-0d1atj/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-0d1atj/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-0d1atj/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-0d1atj/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-0d1atj/apt_archive ./ Sources [496 B]
Get:5 copy:/<<BUILDDIR>>/resolver-0d1atj/apt_archive ./ Packages [575 B]
Fetched 2404 B in 1s (3241 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-0d1atj/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-0d1atj/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
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 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 sensible-utils 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 sensible-utils
zlib1g-dev
0 upgraded, 34 newly installed, 0 to remove and 4 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-0d1atj/apt_archive ./ sbuild-build-depends-kma-dummy 0.invalid.0 [868 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 1.5.2-2 [29.6 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 sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-3 [801 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.2 [187 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.64.3-2 [1158 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-2 [8286 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-5+b1 [593 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.2 [1007 kB]
Get:34 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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Selecting previously unselected package libuchardet0:armhf.
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Setting up libpipeline1:armhf (1.5.2-2) ...
Setting up libicu67:armhf (67.1-2) ...
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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) ...
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Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libxml2:armhf (2.9.10+dfsg-5+b1) ...
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 (1:1.16.2-3) ...
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) ...
Setting up sbuild-build-depends-kma-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.30-8+rpi1) ...
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.34-8+rpi1 dpkg-dev_1.19.7 g++-9_9.3.0-14+rpi1 gcc-9_9.3.0-14+rpi1 libc6-dev_2.30-8+rpi1 libstdc++-9-dev_9.3.0-14+rpi1 libstdc++6_10.1.0-4+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_2.1.6 autoconf_2.69-11.1 automake_1:1.16.2-3 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-8+rpi1 binutils-arm-linux-gnueabihf_2.34-8+rpi1 binutils-common_2.34-8+rpi1 bsdextrautils_2.35.2-6 bsdutils_1:2.35.2-6 build-essential_12.8 bzip2_1.0.8-3 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.3.0-14+rpi1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dmsetup_2:1.02.167-1+b2 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.35.2-6 file_1:5.38-5 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.3.0-14+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-10-base_10.1.0-4+rpi1 gcc-9_9.3.0-14+rpi1 gcc-9-base_9.3.0-14+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-3 libacl1_2.2.53-8 libapt-pkg6.0_2.1.6 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.2 libasan5_9.3.0-14+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.1.0-4+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libbinutils_2.34-8+rpi1 libblkid1_2.35.2-6 libbz2-1.0_1.0.8-3 libc-bin_2.30-8+rpi1 libc-dev-bin_2.30-8+rpi1 libc6_2.30-8+rpi1 libc6-dev_2.30-8+rpi1 libcap-ng0_0.7.9-2.2 libcap2_1:2.36-1 libcap2-bin_1:2.36-1 libcc1-0_10.1.0-4+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libcryptsetup12_2:2.3.3-1 libctf-nobfd0_2.34-8+rpi1 libctf0_2.34-8+rpi1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.252 libdebhelper-perl_13.2 libdevmapper1.02.1_2:1.02.167-1+b2 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.35.2-6 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-9-dev_9.3.0-14+rpi1 libgcc-s1_10.1.0-4+rpi1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.3-2 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.14-2 libgomp1_10.1.0-4+rpi1 libgpg-error0_1.38-2 libhogweed5_3.5.1+really3.5.1-2 libicu67_67.1-2 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libjson-c4_0.13.1+dfsg-9 libksba8_1.4.0-2 libldap-2.4-2_2.4.50+dfsg-1 libldap-common_2.4.50+dfsg-1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.35.2-6 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 libnpth0_1.6-2 libp11-kit0_0.23.20-1 libpam-cap_1:2.36-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.30_5.30.3-4 libpipeline1_1.5.2-2 libreadline7_7.0-5 libreadline8_8.0-4 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+rpi1 libselinux1_3.0-1+b1 libsemanage-common_3.0-1 libsemanage1_3.0-1+b1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.35.2-6 libsqlite3-0_3.32.3-1 libss2_1.45.6-1 libssl1.1_1.1.1g-1 libstdc++-9-dev_9.3.0-14+rpi1 libstdc++6_10.1.0-4+rpi1 libsub-override-perl_0.09-2 libsystemd0_245.6-2+rpi1 libtasn1-6_4.16.0-2 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10.1.0-4+rpi1 libuchardet0_0.0.7-1 libudev1_245.6-2+rpi1 libunistring2_0.9.10-4 libuuid1_2.35.2-6 libxml2_2.9.10+dfsg-5+b1 libzstd1_1.4.5+dfsg-3+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-2 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.35.2-6 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_2.96-3 tar_1.30+dfsg-7 tzdata_2020a-1 util-linux_2.35.2-6 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 '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Mon Jul 13 21:55:44 2020 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_1.3.2-1.dsc
dpkg-source: info: extracting kma in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking kma_1.3.2.orig.tar.bz2
dpkg-source: info: unpacking kma_1.3.2-1.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-ae703480-aac7-4c93-a776-a97b1f999e8a
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 1.3.2-1
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 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:468:55: note: in expansion of macro 'getNuc'
468 | 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:483:51: note: in expansion of macro 'getNuc'
483 | 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:513:56: note: in expansion of macro 'getNuc'
513 | 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:527:52: note: in expansion of macro 'getNuc'
527 | 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:818:55: note: in expansion of macro 'getNuc'
818 | 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:833:51: note: in expansion of macro 'getNuc'
833 | 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:876:56: note: in expansion of macro 'getNuc'
876 | 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:889:52: note: in expansion of macro 'getNuc'
889 | 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:1008:55: note: in expansion of macro 'getNuc'
1008 | 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:1023:51: note: in expansion of macro 'getNuc'
1023 | 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:1059:56: note: in expansion of macro 'getNuc'
1059 | 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:1072:52: note: in expansion of macro 'getNuc'
1072 | 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: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 decon.o decon.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 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
kma.c: In function 'kma_main':
kma.c:1143:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1143 | fread(&qseq.len, sizeof(int), 1, templatefile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
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
kma.c:1138:34: 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:385:15: note: in a call to function 'strlen' declared here
385 | extern size_t strlen (const char *__s)
| ^~~~~~
kma.c:1184:32: warning: argument 1 null where non-null expected [-Wnonnull]
1184 | 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:1190:32: warning: argument 1 null where non-null expected [-Wnonnull]
1190 | 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:1202:32: warning: argument 1 null where non-null expected [-Wnonnull]
1202 | 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 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
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 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
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
mt1.c: In function 'runKMA_Mt1':
mt1.c:178:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
178 | fread(&DB_size, sizeof(int), 1, 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 pherror.o pherror.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:450:11: note: in expansion of macro 'getNuc'
450 | 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:577:27: note: in expansion of macro 'getNuc'
577 | 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:585:28: 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:593:27: note: in expansion of macro 'getNuc'
593 | 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:740:11: note: in expansion of macro 'getNuc'
740 | 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:994:11: note: in expansion of macro 'getNuc'
994 | 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 printconsensus.o printconsensus.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 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:576:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
576 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:577:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
577 | fread(header->seq, 1, header->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:578:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
578 | fread(best_start_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:579:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
579 | fread(best_end_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:580:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
580 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:675:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
675 | fread(stats, sizeof(int), 3, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:679:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
679 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:680:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
680 | fread(header->seq, 1, header->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:724:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
724 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:777:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
777 | fread(stats, sizeof(int), 2, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:820:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
820 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:844:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
844 | fread(stats, sizeof(int), 2, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:860:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
860 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:861:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
861 | fread(header->seq, 1, header->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:862:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
862 | fread(best_start_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:863:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
863 | fread(best_end_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:864:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
864 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1010:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1010 | fread(stats, sizeof(int), 3, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1014:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1014 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1015:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1015 | fread(header->seq, 1, header->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c: In function 'runKMA_MEM':
runkma.c:1658:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1658 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1659:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1659 | fread(header->seq, 1, header->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1660:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1660 | fread(best_start_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1661:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1661 | fread(best_end_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1662:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1662 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1757:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1757 | fread(stats, sizeof(int), 3, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1761:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1761 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1762:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1762 | fread(header->seq, 1, header->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1806:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1806 | 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:1902:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1902 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1926:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1926 | fread(stats, sizeof(int), 2, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1942:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1942 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1943:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1943 | fread(header->seq, 1, header->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1944:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1944 | fread(best_start_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1945:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1945 | fread(best_end_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1946:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1946 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:2089:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
2089 | fread(stats, sizeof(int), 3, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:2093:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
2093 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:2094:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
2094 | 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:875:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
875 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:876:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
876 | fread(header->seq, 1, header->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:877:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
877 | fread(best_start_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:878:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
878 | fread(best_end_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:879:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
879 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:974:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
974 | fread(stats, sizeof(int), 3, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:978:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
978 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:979:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
979 | fread(header->seq, 1, header->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1023:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1023 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1076:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1076 | fread(stats, sizeof(int), 2, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1119:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1119 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1143:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1143 | fread(stats, sizeof(int), 2, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1159:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1159 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1160:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1160 | fread(header->seq, 1, header->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1161:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1161 | fread(best_start_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1162:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1162 | fread(best_end_pos, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1163:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1163 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1307:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1307 | fread(stats, sizeof(int), 3, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1311:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1311 | fread(qseq->seq, 1, qseq->len, frag_in_raw);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spltdb.c:1312:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
1312 | 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
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
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)];
| ^~~~~~
ar -csru libkma.a align.o alnfrags.o ankers.o assembly.o chain.o compdna.o compkmers.o compress.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 265989 new size 267474
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_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_1.3.2-1_armhf.deb'.
dpkg-deb: building package 'kma-dbgsym' in '../kma-dbgsym_1.3.2-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../kma_1.3.2-1_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 2020-07-19T05:33:12Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
kma_1.3.2-1_armhf.changes:
--------------------------
Format: 1.8
Date: Mon, 13 Jul 2020 23:54:45 +0200
Source: kma
Binary: kma kma-dbgsym
Architecture: armhf
Version: 1.3.2-1
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 (1.3.2-1) unstable; urgency=medium
.
* Team upload.
* New upstream version
Checksums-Sha1:
9d921b43a289e703637f4beec3f57551f73c4945 379648 kma-dbgsym_1.3.2-1_armhf.deb
3af9812c5da80889e003b45b779ed74dd74faf2c 4657 kma_1.3.2-1_armhf.buildinfo
8ca3eeee80dc66c6bab698683801e5e4618c6d22 111316 kma_1.3.2-1_armhf.deb
Checksums-Sha256:
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38290380faa17dad36a1677e3ef4d3fb695c6ae550b97e27aee3a286a00a6261 4657 kma_1.3.2-1_armhf.buildinfo
7878079ac7fd6fa0dece19128d2c24386851b498886dc0768a1f3ea23bdd938b 111316 kma_1.3.2-1_armhf.deb
Files:
4beab05f4ab404bb5043b7819ec0d6c4 379648 debug optional kma-dbgsym_1.3.2-1_armhf.deb
b9a81d8f5bcc3b0e25e77d1395080fcc 4657 science optional kma_1.3.2-1_armhf.buildinfo
a517e0ae82fcfda4808db5576bff5279 111316 science optional kma_1.3.2-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
kma-dbgsym_1.3.2-1_armhf.deb
----------------------------
new Debian package, version 2.0.
size 379648 bytes: control archive=696 bytes.
436 bytes, 12 lines control
401 bytes, 4 lines md5sums
Package: kma-dbgsym
Source: kma
Version: 1.3.2-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 416
Depends: kma (= 1.3.2-1)
Section: debug
Priority: optional
Description: debug symbols for kma
Build-Ids: 2fc7e3f3e2819360e2d992d6cee1612e06401556 63255bc2f55d472685a0c8c9b910487519154983 e50fa005bd4d98b6019f8589b3d13e4bfcd8ffd0
drwxr-xr-x root/root 0 2020-07-13 21:54 ./
drwxr-xr-x root/root 0 2020-07-13 21:54 ./usr/
drwxr-xr-x root/root 0 2020-07-13 21:54 ./usr/lib/
drwxr-xr-x root/root 0 2020-07-13 21:54 ./usr/lib/debug/
drwxr-xr-x root/root 0 2020-07-13 21:54 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2020-07-13 21:54 ./usr/lib/debug/.build-id/2f/
-rw-r--r-- root/root 19144 2020-07-13 21:54 ./usr/lib/debug/.build-id/2f/c7e3f3e2819360e2d992d6cee1612e06401556.debug
drwxr-xr-x root/root 0 2020-07-13 21:54 ./usr/lib/debug/.build-id/63/
-rw-r--r-- root/root 379668 2020-07-13 21:54 ./usr/lib/debug/.build-id/63/255bc2f55d472685a0c8c9b910487519154983.debug
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-rw-r--r-- root/root 7964 2020-07-13 21:54 ./usr/lib/debug/.build-id/e5/0fa005bd4d98b6019f8589b3d13e4bfcd8ffd0.debug
drwxr-xr-x root/root 0 2020-07-13 21:54 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2020-07-13 21:54 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 3880 2020-07-13 21:54 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/kma.debug
drwxr-xr-x root/root 0 2020-07-13 21:54 ./usr/share/
drwxr-xr-x root/root 0 2020-07-13 21:54 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-07-13 21:54 ./usr/share/doc/kma-dbgsym -> kma
kma_1.3.2-1_armhf.deb
---------------------
new Debian package, version 2.0.
size 111316 bytes: control archive=1068 bytes.
882 bytes, 17 lines control
543 bytes, 9 lines md5sums
Package: kma
Version: 1.3.2-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 296
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 2020-07-13 21:54 ./
drwxr-xr-x root/root 0 2020-07-13 21:54 ./usr/
drwxr-xr-x root/root 0 2020-07-13 21:54 ./usr/bin/
-rwxr-xr-x root/root 263884 2020-07-13 21:54 ./usr/bin/kma
-rwxr-xr-x root/root 5668 2020-07-13 21:54 ./usr/bin/kma_index
-rwxr-xr-x root/root 13912 2020-07-13 21:54 ./usr/bin/kma_shm
drwxr-xr-x root/root 0 2020-07-13 21:54 ./usr/share/
drwxr-xr-x root/root 0 2020-07-13 21:54 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-07-13 21:54 ./usr/share/doc/kma/
-rw-r--r-- root/root 2947 2020-07-10 09:02 ./usr/share/doc/kma/README.md.gz
-rw-r--r-- root/root 609 2020-07-13 21:54 ./usr/share/doc/kma/changelog.Debian.gz
-rw-r--r-- root/root 952 2020-07-13 21:54 ./usr/share/doc/kma/copyright
drwxr-xr-x root/root 0 2020-07-13 21:54 ./usr/share/man/
drwxr-xr-x root/root 0 2020-07-13 21:54 ./usr/share/man/man1/
-rw-r--r-- root/root 1312 2020-07-13 21:54 ./usr/share/man/man1/kma.1.gz
-rw-r--r-- root/root 697 2020-07-13 21:54 ./usr/share/man/man1/kma_index.1.gz
-rw-r--r-- root/root 426 2020-07-13 21:54 ./usr/share/man/man1/kma_shm.1.gz
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| Post Build |
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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: 8612
Build-Time: 82
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 290
Job: kma_1.3.2-1
Machine Architecture: armhf
Package: kma
Package-Time: 422
Source-Version: 1.3.2-1
Space: 8612
Status: successful
Version: 1.3.2-1
--------------------------------------------------------------------------------
Finished at 2020-07-19T05:33:12Z
Build needed 00:07:02, 8612k disc space