kma →
1.2.11-1 →
armhf → 2019-09-06 11:10:07
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02
+==============================================================================+
| kma 1.2.11-1 (armhf) Fri, 06 Sep 2019 11:01:55 +0000 |
+==============================================================================+
Package: kma
Version: 1.2.11-1
Source Version: 1.2.11-1
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-5c6bb5b3-255e-4d2b-9e6f-094a438f225f' 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 [13.0 MB]
Fetched 24.5 MB in 26s (928 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 729 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main kma 1.2.11-1 (dsc) [1918 B]
Get:2 http://172.17.0.1/private bullseye-staging/main kma 1.2.11-1 (tar) [723 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main kma 1.2.11-1 (diff) [4912 B]
Fetched 729 kB in 0s (6010 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/kma-f3aUJ8/kma-1.2.11' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/kma-f3aUJ8' 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-fN7ET0/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-fN7ET0/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-fN7ET0/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-fN7ET0/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-fN7ET0/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-fN7ET0/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-fN7ET0/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-fN7ET0/apt_archive ./ Packages [430 B]
Fetched 2106 B in 1s (2619 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 96 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-fN7ET0/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (15.6 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12050 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-fN7ET0/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-fN7ET0/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-fN7ET0/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-fN7ET0/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-fN7ET0/apt_archive ./ Sources [496 B]
Get:5 copy:/<<BUILDDIR>>/resolver-fN7ET0/apt_archive ./ Packages [576 B]
Fetched 2405 B in 1s (3109 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install kma build dependencies (apt-based resolver)
---------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libelf1
libfile-stripnondeterminism-perl libglib2.0-0 libicu63 libmagic-mgc
libmagic1 libncurses6 libncursesw6 libpipeline1 libsigsegv2
libsub-override-perl libtinfo5 libtinfo6 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 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
The following packages will be upgraded:
libncursesw6 libtinfo6
2 upgraded, 37 newly installed, 0 to remove and 94 not upgraded.
Need to get 19.1 MB of archives.
After this operation, 67.4 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-fN7ET0/apt_archive ./ sbuild-build-depends-kma-dummy 0.invalid.0 [864 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 2.8.7-3 [1254 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libtinfo6 armhf 6.1+20190803-1 [318 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libncursesw6 armhf 6.1+20190803-1 [104 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12 [15.8 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.37-5 [253 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.37-5 [111 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.37-5 [66.2 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-2 [185 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-9 [547 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.5.0-1 [22.8 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.5.0-1 [14.1 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-1 [69.7 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.60.6-2 [1109 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+b2 [571 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.1+20190803-1 [79.3 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.5.4 [1035 kB]
Get:39 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
Fetched 19.1 MB in 2s (9923 kB/s)
Selecting previously unselected package libbsd0:armhf.
(Reading database ... 12050 files and directories currently installed.)
Preparing to unpack .../0-libbsd0_0.10.0-1_armhf.deb ...
Unpacking libbsd0:armhf (0.10.0-1) ...
Selecting previously unselected package libtinfo5:armhf.
Preparing to unpack .../1-libtinfo5_6.1+20190803-1_armhf.deb ...
Unpacking libtinfo5:armhf (6.1+20190803-1) ...
Selecting previously unselected package bsdmainutils.
Preparing to unpack .../2-bsdmainutils_11.1.2_armhf.deb ...
Unpacking bsdmainutils (11.1.2) ...
Selecting previously unselected package libuchardet0:armhf.
Preparing to unpack .../3-libuchardet0_0.0.6-3_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.6-3) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../4-groff-base_1.22.4-3_armhf.deb ...
Unpacking groff-base (1.22.4-3) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../5-libpipeline1_1.5.1-2_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.1-2) ...
Selecting previously unselected package man-db.
Preparing to unpack .../6-man-db_2.8.7-3_armhf.deb ...
Unpacking man-db (2.8.7-3) ...
Preparing to unpack .../7-libtinfo6_6.1+20190803-1_armhf.deb ...
Unpacking libtinfo6:armhf (6.1+20190803-1) over (6.1+20181013-2) ...
Setting up libtinfo6:armhf (6.1+20190803-1) ...
(Reading database ... 12691 files and directories currently installed.)
Preparing to unpack .../libncursesw6_6.1+20190803-1_armhf.deb ...
Unpacking libncursesw6:armhf (6.1+20190803-1) over (6.1+20181013-2) ...
Setting up libncursesw6:armhf (6.1+20190803-1) ...
Selecting previously unselected package sensible-utils.
(Reading database ... 12691 files and directories currently installed.)
Preparing to unpack .../00-sensible-utils_0.0.12_all.deb ...
Unpacking sensible-utils (0.0.12) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../01-libmagic-mgc_1%3a5.37-5_armhf.deb ...
Unpacking libmagic-mgc (1:5.37-5) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../02-libmagic1_1%3a5.37-5_armhf.deb ...
Unpacking libmagic1:armhf (1:5.37-5) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.37-5_armhf.deb ...
Unpacking file (1:5.37-5) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../04-gettext-base_0.19.8.1-9_armhf.deb ...
Unpacking gettext-base (0.19.8.1-9) ...
Selecting previously unselected package libsigsegv2:armhf.
Preparing to unpack .../05-libsigsegv2_2.12-2_armhf.deb ...
Unpacking libsigsegv2:armhf (2.12-2) ...
Selecting previously unselected package m4.
Preparing to unpack .../06-m4_1.4.18-2_armhf.deb ...
Unpacking m4 (1.4.18-2) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../07-autoconf_2.69-11_all.deb ...
Unpacking autoconf (2.69-11) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../08-autotools-dev_20180224.1_all.deb ...
Unpacking autotools-dev (20180224.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../09-automake_1%3a1.16.1-4_all.deb ...
Unpacking automake (1:1.16.1-4) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../10-autopoint_0.19.8.1-9_all.deb ...
Unpacking autopoint (0.19.8.1-9) ...
Selecting previously unselected package libtool.
Preparing to unpack .../11-libtool_2.4.6-9_all.deb ...
Unpacking libtool (2.4.6-9) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../12-dh-autoreconf_19_all.deb ...
Unpacking dh-autoreconf (19) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../13-libarchive-zip-perl_1.64-1_all.deb ...
Unpacking libarchive-zip-perl (1.64-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../14-libsub-override-perl_0.09-2_all.deb ...
Unpacking libsub-override-perl (0.09-2) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../15-libfile-stripnondeterminism-perl_1.5.0-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.5.0-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../16-dh-strip-nondeterminism_1.5.0-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.5.0-1) ...
Selecting previously unselected package libelf1:armhf.
Preparing to unpack .../17-libelf1_0.176-1.1_armhf.deb ...
Unpacking libelf1:armhf (0.176-1.1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../18-dwz_0.13-1_armhf.deb ...
Unpacking dwz (0.13-1) ...
Selecting previously unselected package libglib2.0-0:armhf.
Preparing to unpack .../19-libglib2.0-0_2.60.6-2_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.60.6-2) ...
Selecting previously unselected package libicu63:armhf.
Preparing to unpack .../20-libicu63_63.2-2_armhf.deb ...
Unpacking libicu63:armhf (63.2-2) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../21-libxml2_2.9.4+dfsg1-7+b2_armhf.deb ...
Unpacking libxml2:armhf (2.9.4+dfsg1-7+b2) ...
Selecting previously unselected package libcroco3:armhf.
Preparing to unpack .../22-libcroco3_0.6.13-1_armhf.deb ...
Unpacking libcroco3:armhf (0.6.13-1) ...
Selecting previously unselected package libncurses6:armhf.
Preparing to unpack .../23-libncurses6_6.1+20190803-1_armhf.deb ...
Unpacking libncurses6:armhf (6.1+20190803-1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../24-gettext_0.19.8.1-9_armhf.deb ...
Unpacking gettext (0.19.8.1-9) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../25-intltool-debian_0.35.0+20060710.5_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.5) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../26-po-debconf_1.0.21_all.deb ...
Unpacking po-debconf (1.0.21) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../27-debhelper_12.5.4_all.deb ...
Unpacking debhelper (12.5.4) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../28-zlib1g-dev_1%3a1.2.11.dfsg-1_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Selecting previously unselected package sbuild-build-depends-kma-dummy.
Preparing to unpack .../29-sbuild-build-depends-kma-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-kma-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.5.1-2) ...
Setting up libmagic-mgc (1:5.37-5) ...
Setting up libarchive-zip-perl (1.64-1) ...
Setting up libglib2.0-0:armhf (2.60.6-2) ...
No schema files found: doing nothing.
Setting up libmagic1:armhf (1:5.37-5) ...
Setting up gettext-base (0.19.8.1-9) ...
Setting up file (1:5.37-5) ...
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 (1.5.0-1) ...
Setting up libtool (2.4.6-9) ...
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 (2.8.7-3) ...
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 (12.5.4) ...
Setting up dh-autoreconf (19) ...
Setting up dh-strip-nondeterminism (1.5.0-1) ...
Setting up sbuild-build-depends-kma-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.28-10+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_2.31.1-16+rpi1 dpkg-dev_1.19.7 g++-8_8.3.0-6+rpi1 gcc-8_8.3.0-6+rpi1 libc6-dev_2.28-10+rpi1 libstdc++-8-dev_8.3.0-6+rpi1 libstdc++6_8.3.0-6+rpi1 linux-libc-dev_4.18.20-2+rpi1
Package versions: adduser_3.118 apt_1.8.2 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.3+rpi1 base-passwd_3.5.46 bash_5.0-4 binutils_2.31.1-16+rpi1 binutils-arm-linux-gnueabihf_2.31.1-16+rpi1 binutils-common_2.31.1-16+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.33.1-0.1 build-essential_12.6 bzip2_1.0.6-9.1 coreutils_8.30-3 cpp_4:8.3.0-1+rpi2 cpp-8_8.3.0-6+rpi1 dash_0.5.10.2-5 debconf_1.5.71 debhelper_12.5.4 debianutils_4.8.6.1 dh-autoreconf_19 dh-strip-nondeterminism_1.5.0-1 diffutils_1:3.7-3 dirmngr_2.2.12-1+rpi1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-1 e2fsprogs_1.44.5-1 fakeroot_1.23-1 fdisk_2.33.1-0.1 file_1:5.37-5 findutils_4.6.0+git+20190209-2 g++_4:8.3.0-1+rpi2 g++-8_8.3.0-6+rpi1 gcc_4:8.3.0-1+rpi2 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+b1 gcc-7-base_7.3.0-19 gcc-8_8.3.0-6+rpi1 gcc-8-base_8.3.0-6+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gnupg_2.2.12-1+rpi1 gnupg-l10n_2.2.12-1+rpi1 gnupg-utils_2.2.12-1+rpi1 gpg_2.2.12-1+rpi1 gpg-agent_2.2.12-1+rpi1 gpg-wks-client_2.2.12-1+rpi1 gpg-wks-server_2.2.12-1+rpi1 gpgconf_2.2.12-1+rpi1 gpgsm_2.2.12-1+rpi1 gpgv_2.2.12-1+rpi1 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3 hostname_3.21 init-system-helpers_1.56+nmu1 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-4 libapt-pkg5.0_1.8.2 libarchive-zip-perl_1.64-1 libasan5_8.3.0-6+rpi1 libassuan0_2.5.2-1 libatomic1_8.3.0-6+rpi1 libattr1_1:2.4.48-4 libaudit-common_1:2.8.4-3 libaudit1_1:2.8.4-3 libbinutils_2.31.1-16+rpi1 libblkid1_2.33.1-0.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.6-9.1 libc-bin_2.28-10+rpi1 libc-dev-bin_2.28-10+rpi1 libc6_2.28-10+rpi1 libc6-dev_2.28-10+rpi1 libcap-ng0_0.7.9-2 libcc1-0_8.3.0-6+rpi1 libcom-err2_1.44.5-1 libcroco3_0.6.13-1 libdb5.3_5.3.28+dfsg1-0.5 libdebconfclient0_0.249 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.5.0-1 libgcc-8-dev_8.3.0-6+rpi1 libgcc1_1:8.3.0-6+rpi1 libgcrypt20_1.8.4-5 libgdbm-compat4_1.18.1-4 libgdbm6_1.18.1-4 libglib2.0-0_2.60.6-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.7-4 libgomp1_8.3.0-6+rpi1 libgpg-error0_1.35-1 libhogweed4_3.4.1-1 libicu63_63.2-2 libidn2-0_2.0.5-1 libisl19_0.20-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.47+dfsg-3+rpi1 libldap-common_2.4.47+dfsg-3+rpi1 liblocale-gettext-perl_1.07-3+b3 liblz4-1_1.8.3-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-5 libmagic1_1:5.37-5 libmount1_2.33.1-0.1 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_0.23.15-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre3_2:8.39-12 libperl5.28_5.28.1-6 libpipeline1_1.5.1-2 libreadline7_7.0-5 libsasl2-2_2.1.27+dfsg-1+b1 libsasl2-modules-db_2.1.27+dfsg-1+b1 libseccomp2_2.3.3-4 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33.1-0.1 libsqlite3-0_3.27.2-3 libss2_1.44.5-1 libstdc++-8-dev_8.3.0-6+rpi1 libstdc++6_8.3.0-6+rpi1 libsub-override-perl_0.09-2 libsystemd0_241-5+rpi1 libtasn1-6_4.13-3 libtext-charwidth-perl_0.04-7.1+b1 libtext-iconv-perl_1.7-5+b10 libtext-wrapi18n-perl_0.06-7.1 libtinfo5_6.1+20190803-1 libtinfo6_6.1+20190803-1 libtool_2.4.6-9 libubsan1_8.3.0-6+rpi1 libuchardet0_0.0.6-3 libudev1_241-5+rpi1 libunistring2_0.9.10-1 libuuid1_2.33.1-0.1 libxml2_2.9.4+dfsg1-7+b2 libzstd1_1.3.8+dfsg-3+rpi1 linux-libc-dev_4.18.20-2+rpi1 login_1:4.5-1.1 lsb-base_10.2019051400+rpi1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.7-3 mawk_1.3.3-17 mount_2.33.1-0.1 ncurses-base_6.1+20181013-2 ncurses-bin_6.1+20181013-2 netbase_5.6 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-6 perl-base_5.28.1-6 perl-modules-5.28_5.28.1-6 pinentry-curses_1.1.0-2 po-debconf_1.0.21 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 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_2.93-8 tar_1.30+dfsg-6 tzdata_2019a-1 util-linux_2.33.1-0.1 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 Sat Aug 31 09:25:43 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_1.2.11-1.dsc
dpkg-source: info: extracting kma in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking kma_1.2.11.orig.tar.bz2
dpkg-source: info: unpacking kma_1.2.11-1.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-5c6bb5b3-255e-4d2b-9e6f-094a438f225f
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package kma
dpkg-buildpackage: info: source version 1.2.11-1
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 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]
#define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
^~
align.c:90:55: note: in expansion of macro 'getNuc'
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]
#define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
^~
align.c:103:51: note: in expansion of macro 'getNuc'
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]
#define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
^~
align.c:143:56: note: in expansion of macro 'getNuc'
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]
#define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
^~
align.c:156:52: note: in expansion of macro 'getNuc'
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]
#define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
^~
align.c:452:54: note: in expansion of macro 'getNuc'
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]
#define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
^~
align.c:467:50: note: in expansion of macro 'getNuc'
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]
#define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
^~
align.c:498:55: note: in expansion of macro 'getNuc'
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]
#define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
^~
align.c:512:51: note: in expansion of macro 'getNuc'
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]
#define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
^~
align.c:780:55: note: in expansion of macro 'getNuc'
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]
#define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
^~
align.c:795:51: note: in expansion of macro 'getNuc'
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]
#define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
^~
align.c:838:56: note: in expansion of macro 'getNuc'
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]
#define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
^~
align.c:851:52: note: in expansion of macro 'getNuc'
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]
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]
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]
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]
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]
#define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
^~
assembly.c:122:72: note: in expansion of macro 'getNuc'
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]
#define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
^~
assembly.c:646:32: note: in expansion of macro 'getNuc'
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]
#define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
^~
assembly.c:820:26: note: in expansion of macro 'getNuc'
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]
fread(buffer, sizeof(int), 8, file);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assembly.c:415:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
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]
fread(header->seq, 1, header->len, file);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assembly.c: In function 'assemble_KMA_dense_threaded':
assembly.c:861:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(buffer, sizeof(int), 8, file);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assembly.c:888:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(qseq->seq, 1, qseq->len, file);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assembly.c:889:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(header->seq, 1, header->len, file);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assembly.c: In function 'skip_assemble_KMA':
assembly.c:1136:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(buffer, sizeof(int), 8, file);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assembly.c:1156:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(qseq->seq, 1, qseq->len, file);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assembly.c:1157:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
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]
#define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
^~
compdna.c:154:12: note: in expansion of macro 'getNuc'
*--seq = getNuc(compressor->seq, i);
^~~~~~
compdna.c: In function 'binRev':
compdna.c:192:15: warning: right shift count >= width of type [-Wshift-count-overflow]
return ((mer >> 32) | (mer << 32));
^~
compdna.c:192:29: warning: left shift count >= width of type [-Wshift-count-overflow]
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]
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:101:8: warning: right shift count >= width of type [-Wshift-count-overflow]
check >>= 32;
^~~
compress.c: In function 'compressKMA_deconDB':
compress.c:886:9: warning: right shift count >= width of type [-Wshift-count-overflow]
check >>= 32;
^~~
compress.c: In function 'compressKMA_deconMegaDB':
compress.c:989:9: warning: right shift count >= width of type [-Wshift-count-overflow]
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
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
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]
#define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
^~
ef.c:82:51: note: in expansion of macro 'getNuc'
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 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
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
hashmapindex.c: In function 'hashMap_index_load':
hashmapindex.c:253:2: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
read(seq, src->seq, ((src->len >> 5) + 1) * sizeof(long unsigned));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hashmapindex.c:254:2: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
read(index, src->index, src->size * sizeof(int));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hashmapindex.c: In function 'hashMap_index_build':
hashmapindex.c:274:2: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
read(seq, src->seq, ((src->len >> 5) + 1) * sizeof(long unsigned));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hashmapindex.c: In function 'alignLoad_shm_initial':
hashmapindex.c:350:2: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
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 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]
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]
fread(deconfiles[deconcount - 1], 1, size - 1, inputfile);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kma.c: In function 'kma_main':
kma.c:1093:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&qseq.len, sizeof(int), 1, templatefile);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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:1088:34: warning: argument 1 null where non-null expected [-Wnonnull]
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
extern size_t strlen (const char *__s)
^~~~~~
kma.c:1132:32: warning: argument 1 null where non-null expected [-Wnonnull]
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
extern size_t strlen (const char *__s)
^~~~~~
kma.c:1138:32: warning: argument 1 null where non-null expected [-Wnonnull]
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
extern size_t strlen (const char *__s)
^~~~~~
kma.c:1150:32: warning: argument 1 null where non-null expected [-Wnonnull]
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
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 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
loadupdate.c: In function 'load_DBs':
loadupdate.c:178:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
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]
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]
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]
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]
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 makeindex.o makeindex.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 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]
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
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]
#define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
^~
nw.c:73:21: note: in expansion of macro 'getNuc'
aligned->t[m] = getNuc(template, nuc_pos);
^~~~~~
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
#define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
^~
nw.c:161:11: note: in expansion of macro 'getNuc'
t_nuc = getNuc(template, nuc_pos);
^~~~~~
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
#define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
^~
nw.c:258:27: note: in expansion of macro 'getNuc'
aligned->t[Stat.len] = getNuc(template, nuc_pos);
^~~~~~
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
#define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
^~
nw.c:266:28: note: in expansion of macro 'getNuc'
aligned->t[Stat.len] = getNuc(template, nuc_pos);
^~~~~~
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
#define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
^~
nw.c:273:27: note: in expansion of macro 'getNuc'
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]
#define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
^~
nw.c:349:21: note: in expansion of macro 'getNuc'
aligned->t[m] = getNuc(template, nuc_pos);
^~~~~~
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
#define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
^~
nw.c:451:11: note: in expansion of macro 'getNuc'
t_nuc = getNuc(template, nuc_pos);
^~~~~~
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
#define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
^~
nw.c:580:27: note: in expansion of macro 'getNuc'
aligned->t[Stat.len] = getNuc(template, nuc_pos);
^~~~~~
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
#define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
^~
nw.c:588:28: note: in expansion of macro 'getNuc'
aligned->t[Stat.len] = getNuc(template, nuc_pos);
^~~~~~
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
#define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
^~
nw.c:596:27: note: in expansion of macro 'getNuc'
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]
#define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
^~
nw.c:743:11: note: in expansion of macro 'getNuc'
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]
#define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
^~
nw.c:997:11: note: in expansion of macro 'getNuc'
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 printconsensus.o printconsensus.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 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]
read(index_in_no, &kmersize, sizeof(int));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:572:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(qseq->seq, 1, qseq->len, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:573:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(header->seq, 1, header->len, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:574:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(best_start_pos, sizeof(int), bestHits, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:575:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(best_end_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]
fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:671:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(stats, sizeof(int), 3, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:675:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(qseq->seq, 1, qseq->len, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:676:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(header->seq, 1, header->len, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:720:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:773:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(stats, sizeof(int), 2, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:816:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:840:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(stats, sizeof(int), 2, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:856:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(qseq->seq, 1, qseq->len, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:857:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(header->seq, 1, header->len, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:858:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(best_start_pos, sizeof(int), bestHits, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:859:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(best_end_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]
fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1006:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(stats, sizeof(int), 3, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1010:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(qseq->seq, 1, qseq->len, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1011:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(header->seq, 1, header->len, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c: In function 'runKMA_MEM':
runkma.c:1344:3: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
read(index_in_no, &kmersize, sizeof(int));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1589:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(qseq->seq, 1, qseq->len, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1590:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(header->seq, 1, header->len, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1591:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(best_start_pos, sizeof(int), bestHits, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1592:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(best_end_pos, sizeof(int), bestHits, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1593:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1688:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(stats, sizeof(int), 3, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1692:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(qseq->seq, 1, qseq->len, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1693:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(header->seq, 1, header->len, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1737:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1790:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(stats, sizeof(int), 2, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1833:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1857:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(stats, sizeof(int), 2, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1873:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(qseq->seq, 1, qseq->len, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1874:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(header->seq, 1, header->len, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1875:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(best_start_pos, sizeof(int), bestHits, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1876:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(best_end_pos, sizeof(int), bestHits, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:1877:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(bestTemplates, sizeof(int), bestHits, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:2023:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(stats, sizeof(int), 3, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:2027:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(qseq->seq, 1, qseq->len, frag_in_raw);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runkma.c:2028:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
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 'save_kmers_chain':
savekmers.c:4777:15: warning: variable 'chainSeqments' set but not used [-Wunused-but-set-variable]
SeqmentTree *chainSeqments;
^~~~~~~~~~~~~
savekmers.c: In function 'loadFsa':
savekmers.c:83:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
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]
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]
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]
#define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
^~
seq2fasta.c:89:19: note: in expansion of macro 'getNuc'
*--seq = bases[getNuc(compseq, j)];
^~~~~~
seq2fasta.c: In function 'printFastaList':
stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow]
#define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
^~
seq2fasta.c:151:20: note: in expansion of macro 'getNuc'
*--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]
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]
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]
fread(dest->exist, 1, size, file);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
shm.c:115:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(dest->values, 1, size, file);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
shm.c:138:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
fread(&tmp, sizeof(unsigned), 1, file);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
update.c:102:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
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]
fread(&tmp, sizeof(unsigned), 1, file);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
update.c:105:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
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]
#define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62)
^~
vcf.c:122:16: note: in expansion of macro 'getNuc'
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 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 231903 new size 234444
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/kma/usr/bin/kma debian/kma/usr/bin/kma_shm were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'kma' in '../kma_1.2.11-1_armhf.deb'.
dpkg-deb: building package 'kma-dbgsym' in '../kma-dbgsym_1.2.11-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../kma_1.2.11-1_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 2019-09-06T11:09:57Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
kma_1.2.11-1_armhf.changes:
---------------------------
Format: 1.8
Date: Sat, 31 Aug 2019 11:18:21 +0200
Source: kma
Binary: kma kma-dbgsym
Architecture: armhf
Version: 1.2.11-1
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 (1.2.11-1) unstable; urgency=medium
.
* Team upload.
* New upstream version
Checksums-Sha1:
6a00484d599f242bf3a6a6f329de85b19948be81 327956 kma-dbgsym_1.2.11-1_armhf.deb
371d078c75f12a53fae8cd8de242071466446904 4441 kma_1.2.11-1_armhf.buildinfo
30c0e24739a1d047b2d302c8009f59f862135fff 95256 kma_1.2.11-1_armhf.deb
Checksums-Sha256:
61694f8c8f3fb55cdb76326faa95124ae18828b53df8f3ed4a6964f5b49869f9 327956 kma-dbgsym_1.2.11-1_armhf.deb
5b17f403f94844f747f790e8f8bc90f1a1a567e9be233969ce49668b042d5999 4441 kma_1.2.11-1_armhf.buildinfo
fd79f5dfd17e380e2d190fa86553d3820d6d092f8d2610f02c1cb5f8ca09ade0 95256 kma_1.2.11-1_armhf.deb
Files:
46c2cc7112c410baf51a22ba4eaac110 327956 debug optional kma-dbgsym_1.2.11-1_armhf.deb
53a623c9c9c96d1e9d3c7b30dc6c15d4 4441 science optional kma_1.2.11-1_armhf.buildinfo
c32036024fc6e6b78dbb5c129f87e224 95256 science optional kma_1.2.11-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
kma-dbgsym_1.2.11-1_armhf.deb
-----------------------------
new Debian package, version 2.0.
size 327956 bytes: control archive=692 bytes.
438 bytes, 12 lines control
401 bytes, 4 lines md5sums
Package: kma-dbgsym
Source: kma
Version: 1.2.11-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 364
Depends: kma (= 1.2.11-1)
Section: debug
Priority: optional
Description: debug symbols for kma
Build-Ids: 823b092af4ee3ac32ea0ecf893402300032a7d19 9deafb152c6135769d2e2753782173842e6ba0d4 e62748d9697ef75f9b8bb090eae8b69b9f4d7e4c
drwxr-xr-x root/root 0 2019-08-31 09:18 ./
drwxr-xr-x root/root 0 2019-08-31 09:18 ./usr/
drwxr-xr-x root/root 0 2019-08-31 09:18 ./usr/lib/
drwxr-xr-x root/root 0 2019-08-31 09:18 ./usr/lib/debug/
drwxr-xr-x root/root 0 2019-08-31 09:18 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2019-08-31 09:18 ./usr/lib/debug/.build-id/82/
-rw-r--r-- root/root 8964 2019-08-31 09:18 ./usr/lib/debug/.build-id/82/3b092af4ee3ac32ea0ecf893402300032a7d19.debug
drwxr-xr-x root/root 0 2019-08-31 09:18 ./usr/lib/debug/.build-id/9d/
-rw-r--r-- root/root 21136 2019-08-31 09:18 ./usr/lib/debug/.build-id/9d/eafb152c6135769d2e2753782173842e6ba0d4.debug
drwxr-xr-x root/root 0 2019-08-31 09:18 ./usr/lib/debug/.build-id/e6/
-rw-r--r-- root/root 322940 2019-08-31 09:18 ./usr/lib/debug/.build-id/e6/2748d9697ef75f9b8bb090eae8b69b9f4d7e4c.debug
drwxr-xr-x root/root 0 2019-08-31 09:18 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2019-08-31 09:18 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 3868 2019-08-31 09:18 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/kma.debug
drwxr-xr-x root/root 0 2019-08-31 09:18 ./usr/share/
drwxr-xr-x root/root 0 2019-08-31 09:18 ./usr/share/doc/
lrwxrwxrwx root/root 0 2019-08-31 09:18 ./usr/share/doc/kma-dbgsym -> kma
kma_1.2.11-1_armhf.deb
----------------------
new Debian package, version 2.0.
size 95256 bytes: control archive=1068 bytes.
882 bytes, 17 lines control
543 bytes, 9 lines md5sums
Package: kma
Version: 1.2.11-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 256
Depends: libc6 (>= 2.4), 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 2019-08-31 09:18 ./
drwxr-xr-x root/root 0 2019-08-31 09:18 ./usr/
drwxr-xr-x root/root 0 2019-08-31 09:18 ./usr/bin/
-rwxr-xr-x root/root 222872 2019-08-31 09:18 ./usr/bin/kma
-rwxr-xr-x root/root 5668 2019-08-31 09:18 ./usr/bin/kma_index
-rwxr-xr-x root/root 13912 2019-08-31 09:18 ./usr/bin/kma_shm
drwxr-xr-x root/root 0 2019-08-31 09:18 ./usr/share/
drwxr-xr-x root/root 0 2019-08-31 09:18 ./usr/share/doc/
drwxr-xr-x root/root 0 2019-08-31 09:18 ./usr/share/doc/kma/
-rw-r--r-- root/root 2989 2019-08-26 06:43 ./usr/share/doc/kma/README.md.gz
-rw-r--r-- root/root 309 2019-08-31 09:18 ./usr/share/doc/kma/changelog.Debian.gz
-rw-r--r-- root/root 952 2019-08-31 09:17 ./usr/share/doc/kma/copyright
drwxr-xr-x root/root 0 2019-08-31 09:18 ./usr/share/man/
drwxr-xr-x root/root 0 2019-08-31 09:18 ./usr/share/man/man1/
-rw-r--r-- root/root 1312 2019-08-31 09:18 ./usr/share/man/man1/kma.1.gz
-rw-r--r-- root/root 697 2019-08-31 09:18 ./usr/share/man/man1/kma_index.1.gz
-rw-r--r-- root/root 426 2019-08-31 09:18 ./usr/share/man/man1/kma_shm.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 7708
Build-Time: 80
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 350
Job: kma_1.2.11-1
Machine Architecture: armhf
Package: kma
Package-Time: 482
Source-Version: 1.2.11-1
Space: 7708
Status: successful
Version: 1.2.11-1
--------------------------------------------------------------------------------
Finished at 2019-09-06T11:09:57Z
Build needed 00:08:02, 7708k disc space