segemehl →
0.3.4-3 →
armhf → 2021-02-28 06:12:31
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| segemehl 0.3.4-3 (armhf) Sun, 28 Feb 2021 06:07:12 +0000 |
+==============================================================================+
Package: segemehl
Version: 0.3.4-3
Source Version: 0.3.4-3
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-2438d2b1-428a-4c68-a7de-02128ae89c4f' 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 [12.2 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [13.2 MB]
Fetched 25.4 MB in 10s (2653 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: 'segemehl' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/segemehl.git
Please use:
git clone https://salsa.debian.org/med-team/segemehl.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 252 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main segemehl 0.3.4-3 (dsc) [2009 B]
Get:2 http://172.17.0.1/private bullseye-staging/main segemehl 0.3.4-3 (tar) [244 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main segemehl 0.3.4-3 (diff) [5940 B]
Fetched 252 kB in 0s (2397 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/segemehl-5INwP5/segemehl-0.3.4' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/segemehl-5INwP5' 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-rJBBqR/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-rJBBqR/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-rJBBqR/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: 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 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: 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-rJBBqR/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-rJBBqR/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-rJBBqR/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-rJBBqR/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-rJBBqR/apt_archive ./ Packages [433 B]
Fetched 2109 B in 0s (9777 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
bsdextrautils libpam-cap netbase sensible-utils
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 49 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-rJBBqR/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 (62.7 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12400 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), pkg-config, libhts-dev, libncurses-dev, zlib1g-dev
Filtered Build-Depends: debhelper-compat (= 12), pkg-config, libhts-dev, libncurses-dev, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-segemehl-dummy' in '/<<BUILDDIR>>/resolver-rJBBqR/apt_archive/sbuild-build-depends-segemehl-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-segemehl-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-rJBBqR/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-rJBBqR/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-rJBBqR/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-rJBBqR/apt_archive ./ Sources [521 B]
Get:5 copy:/<<BUILDDIR>>/resolver-rJBBqR/apt_archive ./ Packages [602 B]
Fetched 2456 B in 0s (10.7 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install segemehl 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 libbrotli1 libcurl3-gnutls
libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1
libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libhts-dev
libhts3 libicu67 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
liblzma-dev libmagic-mgc libmagic1 libncurses-dev libncurses6 libnghttp2-14
libpipeline1 libpsl5 librtmp1 libsigsegv2 libssh2-1 libssl1.1
libsub-override-perl libtool libuchardet0 libxml2 m4 man-db pkg-config
po-debconf zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff libcurl4-doc libgnutls28-dev
libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev krb5-doc
krb5-user liblzma-doc ncurses-doc libtool-doc gfortran | fortran95-compiler
gcj-jdk m4-doc apparmor less www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs krb5-locales libgpm2 publicsuffix 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 libbrotli1 libcurl3-gnutls
libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1
libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libhts-dev
libhts3 libicu67 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
liblzma-dev libmagic-mgc libmagic1 libncurses-dev libncurses6 libnghttp2-14
libpipeline1 libpsl5 librtmp1 libsigsegv2 libssh2-1 libssl1.1
libsub-override-perl libtool libuchardet0 libxml2 m4 man-db pkg-config
po-debconf sbuild-build-depends-segemehl-dummy zlib1g-dev
0 upgraded, 53 newly installed, 0 to remove and 49 not upgraded.
Need to get 26.7 MB of archives.
After this operation, 85.4 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-rJBBqR/apt_archive ./ sbuild-build-depends-segemehl-dummy 0.invalid.0 [888 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 1.22.4-6 [793 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.4-1 [1307 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-14 [313 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.3-2 [814 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.3.3 [189 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.11.0-1 [15.3 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.183-1 [161 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13+20210201-1 [164 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-6 [8289 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.3 [580 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.3.3 [1011 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.18.3-4 [62.3 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.18.3-4 [108 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6.1-2 [14.5 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1j-1 [1273 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.18.3-4 [315 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.18.3-4 [142 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.43.0-1 [65.3 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.9.0-2 [141 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.74.0-1.1 [301 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libcurl4-gnutls-dev armhf 7.74.0-1.1 [375 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.7-1 [44.0 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libdeflate-dev armhf 1.7-1 [40.3 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.66.7-1 [1182 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libhts3 armhf 1.11-4 [324 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.5-1.0 [219 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libhts-dev armhf 1.11-4 [3815 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.2+20201114-2 [79.9 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libncurses-dev armhf 6.2+20201114-2 [288 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
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Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up libkeyutils1:armhf (1.6.1-2) ...
Setting up libpsl5:armhf (0.21.0-1.2) ...
Setting up libicu67:armhf (67.1-6) ...
Setting up libmagic-mgc (1:5.39-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.66.7-1) ...
No schema files found: doing nothing.
Setting up libssl1.1:armhf (1.1.1j-1) ...
Setting up libdebhelper-perl (13.3.3) ...
Setting up libbrotli1:armhf (1.0.9-2+b1) ...
Setting up libnghttp2-14:armhf (1.43.0-1) ...
Setting up libmagic1:armhf (1:5.39-3) ...
Setting up libdeflate0:armhf (1.7-1) ...
Setting up gettext-base (0.21-4) ...
Setting up file (1:5.39-3) ...
Setting up libkrb5support0:armhf (1.18.3-4) ...
Setting up autotools-dev (20180224.1+nmu1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libncurses6:armhf (6.2+20201114-2) ...
Setting up libsigsegv2:armhf (2.13-1) ...
Setting up autopoint (0.21-4) ...
Setting up pkg-config (0.29.2-1) ...
Setting up libk5crypto3:armhf (1.18.3-4) ...
Setting up liblzma-dev:armhf (5.2.5-1.0) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.9.0-2) ...
Setting up libkrb5-3:armhf (1.18.3-4) ...
Setting up libdeflate-dev:armhf (1.7-1) ...
Setting up libelf1:armhf (0.183-1) ...
Setting up libxml2:armhf (2.9.10+dfsg-6.3) ...
Setting up libfile-stripnondeterminism-perl (1.11.0-1) ...
Setting up libncurses-dev:armhf (6.2+20201114-2) ...
Setting up gettext (0.21-4) ...
Setting up libtool (2.4.6-15) ...
Setting up m4 (1.4.18-5) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libgssapi-krb5-2:armhf (1.18.3-4) ...
Setting up autoconf (2.69-14) ...
Setting up dh-strip-nondeterminism (1.11.0-1) ...
Setting up dwz (0.13+20210201-1) ...
Setting up groff-base (1.22.4-6) ...
Setting up automake (1:1.16.3-2) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libcurl3-gnutls:armhf (7.74.0-1.1) ...
Setting up libcurl4-gnutls-dev:armhf (7.74.0-1.1) ...
Setting up man-db (2.9.4-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up dh-autoreconf (20) ...
Setting up libhts3:armhf (1.11-4) ...
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Setting up debhelper (13.3.3) ...
Setting up sbuild-build-depends-segemehl-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-9+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-76-generic armhf (armv8l)
Toolchain package versions: binutils_2.35.1-7+rpi1 dpkg-dev_1.20.7.1+rpi1 g++-10_10.2.1-6+rpi1 gcc-10_10.2.1-6+rpi1 libc6-dev_2.31-3+rpi1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 linux-libc-dev_5.10.9-1+rpi1
Package versions: adduser_3.118 apt_2.1.18 autoconf_2.69-14 automake_1:1.16.3-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_11+rpi1 base-passwd_3.5.48 bash_5.1-2 binutils_2.35.1-7+rpi1 binutils-arm-linux-gnueabihf_2.35.1-7+rpi1 binutils-common_2.35.1-7+rpi1 bsdextrautils_2.36.1-6 bsdutils_1:2.36.1-6 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.2.1-6+rpi1 dash_0.5.11+git20200708+dd9ef66-5 debconf_1.5.74 debhelper_13.3.3 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.11.0-1 diffutils_1:3.7-5 dirmngr_2.2.20-1 dpkg_1.20.7.1+rpi1 dpkg-dev_1.20.7.1+rpi1 dwz_0.13+20210201-1 e2fsprogs_1.45.7-1 fakeroot_1.25.3-1.1 fdisk_2.36.1-6 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.2.1-6+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.2.1-6+rpi1 gcc-10-base_10.2.1-6+rpi1 gettext_0.21-4 gettext-base_0.21-4 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_3.6-1 groff-base_1.22.4-6 gzip_1.10-2 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20200821-2 libacl1_2.2.53-10 libapt-pkg6.0_2.1.18 libarchive-zip-perl_1.68-1 libasan6_10.2.1-6+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.1-6+rpi1 libattr1_1:2.4.48-6 libaudit-common_1:3.0-2 libaudit1_1:3.0-2 libbinutils_2.35.1-7+rpi1 libblkid1_2.36.1-6 libbrotli1_1.0.9-2+b1 libbz2-1.0_1.0.8-4 libc-bin_2.31-9+rpi1 libc-dev-bin_2.31-3+rpi1 libc6_2.31-3+rpi1 libc6-dev_2.31-3+rpi1 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_10.2.1-6+rpi1 libcom-err2_1.45.7-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.1-7+rpi1 libctf0_2.35.1-7+rpi1 libcurl3-gnutls_7.74.0-1.1 libcurl4-gnutls-dev_7.74.0-1.1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.256 libdebhelper-perl_13.3.3 libdeflate-dev_1.7-1 libdeflate0_1.7-1 libdpkg-perl_1.20.7.1+rpi1 libelf1_0.183-1 libext2fs2_1.45.7-1 libfakeroot_1.25.3-1.1 libfdisk1_2.36.1-6 libffi7_3.3-5 libfile-stripnondeterminism-perl_1.11.0-1 libgcc-10-dev_10.2.1-6+rpi1 libgcc-s1_10.2.1-6+rpi1 libgcrypt20_1.8.7-2 libgdbm-compat4_1.19-2 libgdbm6_1.19-2 libglib2.0-0_2.66.7-1 libgmp10_2:6.2.1+dfsg-1 libgnutls30_3.7.0-5 libgomp1_10.2.1-6+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.18.3-4 libhogweed6_3.6-2 libhts-dev_1.11-4 libhts3_1.11-4 libicu67_67.1-6 libidn2-0_2.3.0-5 libisl23_0.23-1 libk5crypto3_1.18.3-4 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-4 libkrb5support0_1.18.3-4 libksba8_1.5.0-3 libldap-2.4-2_2.4.57+dfsg-1 libldap-common_2.4.57+dfsg-1 liblz4-1_1.9.3-1+rpi1 liblzma-dev_5.2.5-1.0 liblzma5_5.2.5-1.0 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.36.1-6 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncurses-dev_6.2+20201114-2 libncurses6_6.2+20201114-2 libncursesw6_6.2+20201114-2 libnettle8_3.6-2 libnghttp2-14_1.43.0-1 libnpth0_1.6-3 libp11-kit0_0.23.22-1 libpam-cap_1:2.44-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.4.0-2 libpam0g_1.4.0-2 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-2 libpipeline1_1.5.3-1 libpsl5_0.21.0-1.2 libreadline8_8.1-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-2+b1 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.36.1-6 libsqlite3-0_3.34.1-1 libss2_1.45.7-1 libssh2-1_1.9.0-2 libssl1.1_1.1.1j-1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.2-5+rpi1 libtasn1-6_4.16.0-2 libtinfo6_6.2+20201114-2 libtool_2.4.6-15 libubsan1_10.2.1-6+rpi1 libuchardet0_0.0.7-1 libudev1_247.2-5+rpi1 libunistring2_0.9.10-4 libuuid1_2.36.1-6 libxml2_2.9.10+dfsg-6.3 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-1 linux-libc-dev_5.10.9-1+rpi1 login_1:4.8.1-1 logsave_1.45.7-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4 man-db_2.9.4-1 mawk_1.3.4.20200120-2 mount_2.36.1-6 ncurses-base_6.2+20201114-2 ncurses-bin_6.2+20201114-2 netbase_6.2 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-2 perl-base_5.32.1-2 perl-modules-5.32_5.32.1-2 pinentry-curses_1.1.0-4 pkg-config_0.29.2-1 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.1-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-segemehl-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.14 sysvinit-utils_2.96-5 tar_1.32+dfsg-1+rpi1 tzdata_2021a-1 util-linux_2.36.1-6 xz-utils_5.2.5-1.0 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.99u6rQkV/trustedkeys.kbx': General error
gpgv: Signature made Thu Feb 18 09:48:35 2021 UTC
gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
gpgv: issuer "npatra974@gmail.com"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./segemehl_0.3.4-3.dsc
dpkg-source: info: extracting segemehl in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking segemehl_0.3.4.orig.tar.xz
dpkg-source: info: unpacking segemehl_0.3.4-3.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying rpath.patch
dpkg-source: info: applying cross.patch
Check disk 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=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-2438d2b1-428a-4c68-a7de-02128ae89c4f
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package segemehl
dpkg-buildpackage: info: source version 0.3.4-3
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>>'
Cleaning...
rm -f -r build segemehl haarz
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
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build -- all
make -j4 "INSTALL=install --strip-program=true" all
make[2]: Entering directory '/<<PKGBUILDDIR>>'
Building... library for source build/md5.o
Building... library for source build/vstack.o
Building... library for source build/queryalign.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/md5.o libs/md5.c
Building... library for source build/annotation.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/vstack.o libs/vstack.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/queryalign.o libs/queryalign.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/annotation.o libs/annotation.c
Building... library for source build/biofiles.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/biofiles.o libs/biofiles.c
In file included from include/stringutils.h:27,
from libs/annotation.c:29:
libs/annotation.c: In function 'bl_annotationitemDestruct':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/annotation.c:149:23: note: in expansion of macro 'FREEMEMORY'
149 | if(item->chromname) FREEMEMORY(space, item->chromname);
| ^~~~~~~~~~
libs/annotation.c:149:3: note: some parts of macro expansion are not guarded by this 'if' clause
149 | if(item->chromname) FREEMEMORY(space, item->chromname);
| ^~
In file included from include/stringutils.h:27,
from libs/annotation.c:29:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/annotation.c:150:18: note: in expansion of macro 'FREEMEMORY'
150 | if(item->name) FREEMEMORY(space, item->name);
| ^~~~~~~~~~
libs/annotation.c:150:3: note: some parts of macro expansion are not guarded by this 'if' clause
150 | if(item->name) FREEMEMORY(space, item->name);
| ^~
In file included from include/stringutils.h:27,
from libs/annotation.c:29:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/annotation.c:151:21: note: in expansion of macro 'FREEMEMORY'
151 | if(item->itemRgb) FREEMEMORY(space, item->itemRgb);
| ^~~~~~~~~~
libs/annotation.c:151:3: note: some parts of macro expansion are not guarded by this 'if' clause
151 | if(item->itemRgb) FREEMEMORY(space, item->itemRgb);
| ^~
In file included from include/stringutils.h:27,
from libs/annotation.c:29:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/annotation.c:152:24: note: in expansion of macro 'FREEMEMORY'
152 | if(item->blockSizes) FREEMEMORY(space, item->blockSizes);
| ^~~~~~~~~~
libs/annotation.c:152:3: note: some parts of macro expansion are not guarded by this 'if' clause
152 | if(item->blockSizes) FREEMEMORY(space, item->blockSizes);
| ^~
In file included from include/stringutils.h:27,
from libs/annotation.c:29:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/annotation.c:153:25: note: in expansion of macro 'FREEMEMORY'
153 | if(item->blockStarts) FREEMEMORY(space, item->blockStarts);
| ^~~~~~~~~~
libs/annotation.c:153:3: note: some parts of macro expansion are not guarded by this 'if' clause
153 | if(item->blockStarts) FREEMEMORY(space, item->blockStarts);
| ^~
In file included from include/stringutils.h:27,
from libs/annotation.c:29:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/annotation.c:154:26: note: in expansion of macro 'FREEMEMORY'
154 | if(item->blockRefseqs) FREEMEMORY(space, item->blockRefseqs);
| ^~~~~~~~~~
libs/annotation.c:154:3: note: some parts of macro expansion are not guarded by this 'if' clause
154 | if(item->blockRefseqs) FREEMEMORY(space, item->blockRefseqs);
| ^~
In file included from include/stringutils.h:27,
from libs/annotation.c:29:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/annotation.c:155:26: note: in expansion of macro 'FREEMEMORY'
155 | if(item->blockStrands) FREEMEMORY(space, item->blockStrands);
| ^~~~~~~~~~
libs/annotation.c:155:3: note: some parts of macro expansion are not guarded by this 'if' clause
155 | if(item->blockStrands) FREEMEMORY(space, item->blockStrands);
| ^~
In file included from include/stringutils.h:27,
from libs/annotation.c:29:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/annotation.c:156:20: note: in expansion of macro 'FREEMEMORY'
156 | if(item->source) FREEMEMORY(space, item->source);
| ^~~~~~~~~~
libs/annotation.c:156:3: note: some parts of macro expansion are not guarded by this 'if' clause
156 | if(item->source) FREEMEMORY(space, item->source);
| ^~
In file included from include/stringutils.h:27,
from libs/annotation.c:29:
libs/annotation.c: In function 'bl_annotationtrackDestruct':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/annotation.c:409:24: note: in expansion of macro 'FREEMEMORY'
409 | if(track->trackname) FREEMEMORY(space, track->trackname);
| ^~~~~~~~~~
libs/annotation.c:409:3: note: some parts of macro expansion are not guarded by this 'if' clause
409 | if(track->trackname) FREEMEMORY(space, track->trackname);
| ^~
In file included from include/stringutils.h:27,
from libs/annotation.c:29:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/annotation.c:410:23: note: in expansion of macro 'FREEMEMORY'
410 | if(track->filename) FREEMEMORY(space, track->filename);
| ^~~~~~~~~~
libs/annotation.c:410:3: note: some parts of macro expansion are not guarded by this 'if' clause
410 | if(track->filename) FREEMEMORY(space, track->filename);
| ^~
In file included from include/stringutils.h:27,
from libs/annotation.c:29:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/annotation.c:411:26: note: in expansion of macro 'FREEMEMORY'
411 | if(track->description) FREEMEMORY(space, track->description);
| ^~~~~~~~~~
libs/annotation.c:411:3: note: some parts of macro expansion are not guarded by this 'if' clause
411 | if(track->description) FREEMEMORY(space, track->description);
| ^~
In file included from include/stringutils.h:27,
from libs/annotation.c:29:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/annotation.c:418:20: note: in expansion of macro 'FREEMEMORY'
418 | if(track->items) FREEMEMORY(space, track->items) ;
| ^~~~~~~~~~
libs/annotation.c:418:3: note: some parts of macro expansion are not guarded by this 'if' clause
418 | if(track->items) FREEMEMORY(space, track->items) ;
| ^~
In file included from include/stringutils.h:27,
from libs/annotation.c:29:
libs/annotation.c: In function 'bl_annotationmultitrackDestruct':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/annotation.c:455:20: note: in expansion of macro 'FREEMEMORY'
455 | if(track->items) FREEMEMORY(space, track->items) ;
| ^~~~~~~~~~
libs/annotation.c:455:3: note: some parts of macro expansion are not guarded by this 'if' clause
455 | if(track->items) FREEMEMORY(space, track->items) ;
| ^~
Building... library for source build/bitVector.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/bitVector.o libs/bitVector.c
Building... library for source build/locus.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/locus.o libs/locus.c
Building... library for source build/seqclip.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/seqclip.o libs/seqclip.c
In file included from include/stringutils.h:27,
from include/biofiles.h:43,
from include/alignment.h:38,
from include/sw.h:38,
from libs/seqclip.c:44:
libs/seqclip.c: In function 'bl_Find3PrimeGreedy':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/seqclip.c:529:9: note: in expansion of macro 'FREEMEMORY'
529 | FREEMEMORY(space, adapter);
| ^~~~~~~~~~
libs/seqclip.c:528:7: note: some parts of macro expansion are not guarded by this 'if' clause
528 | if(adapter)
| ^~
Building... library for source build/debug.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/debug.o libs/debug.c
Building... library for source build/merge.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/merge.o libs/merge.c
In file included from include/stringutils.h:27,
from libs/merge.c:34:
libs/merge.c: In function 'se_mergeWorker':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/merge.c:1096:20: note: in expansion of macro 'FREEMEMORY'
1096 | if(curkey) FREEMEMORY(NULL, curkey);
| ^~~~~~~~~~
libs/merge.c:1096:9: note: some parts of macro expansion are not guarded by this 'if' clause
1096 | if(curkey) FREEMEMORY(NULL, curkey);
| ^~
In file included from include/stringutils.h:27,
from libs/merge.c:34:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/merge.c:1216:26: note: in expansion of macro 'FREEMEMORY'
1216 | if(!reads && curkey) FREEMEMORY(NULL, curkey);
| ^~~~~~~~~~
libs/merge.c:1216:5: note: some parts of macro expansion are not guarded by this 'if' clause
1216 | if(!reads && curkey) FREEMEMORY(NULL, curkey);
| ^~
Building... library for source build/kdseed.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/kdseed.o libs/kdseed.c
Building... library for source build/stack.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/stack.o libs/stack.c
Building... library for source build/bamio.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/bamio.o libs/bamio.c
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from include/bamio.h:21,
from libs/bamio.c:32:
libs/bamio.c: In function 'bl_bamCrossSectionDestruct':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/bamio.c:468:20: note: in expansion of macro 'FREEMEMORY'
468 | if(cs->x[k].n) FREEMEMORY(NULL, cs->x[k].d);
| ^~~~~~~~~~
libs/bamio.c:468:5: note: some parts of macro expansion are not guarded by this 'if' clause
468 | if(cs->x[k].n) FREEMEMORY(NULL, cs->x[k].d);
| ^~
Building... library for source build/vqueue.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/vqueue.o libs/vqueue.c
Building... library for source build/aluruSort.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/aluruSort.o libs/aluruSort.c
Building... library for source build/segemehl_helper.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/segemehl_helper.o libs/segemehl_helper.c
Building... library for source build/bitArray.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/bitArray.o libs/bitArray.c
Building... library for source build/samheader.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/samheader.o libs/samheader.c
Building... library for source build/sw.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/sw.o libs/sw.c
Building... library for source build/fileio.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/fileio.o libs/fileio.c
Building... library for source build/kdchain.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/kdchain.o libs/kdchain.c
Building... library for source build/vtprogressbar.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/vtprogressbar.o libs/vtprogressbar.c
Building... library for source build/karlin.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/karlin.o libs/karlin.c
Building... library for source build/bgzip.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/bgzip.o libs/bgzip.c
Building... library for source build/gzidx.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/gzidx.o libs/gzidx.c
Building... library for source build/portable_endian.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/portable_endian.o libs/portable_endian.c
Building... library for source build/container.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/container.o libs/container.c
Building... library for source build/bedfiles.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/bedfiles.o libs/bedfiles.c
Building... library for source build/segemehl.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/segemehl.o libs/segemehl.c
Building... library for source build/memory.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/memory.o libs/memory.c
Building... library for source build/junctions.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/junctions.o libs/junctions.c
Building... library for source build/pigeon.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/pigeon.o libs/pigeon.c
Building... library for source build/radixsort.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/radixsort.o libs/radixsort.c
Building... library for source build/sort.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/sort.o libs/sort.c
In file included from include/stringutils.h:27,
from include/biofiles.h:43,
from include/segemehl.h:44,
from libs/pigeon.c:35:
libs/pigeon.c: In function 'pigeon':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/pigeon.c:352:13: note: in expansion of macro 'FREEMEMORY'
352 | if(check) FREEMEMORY(space, check);
| ^~~~~~~~~~
libs/pigeon.c:352:3: note: some parts of macro expansion are not guarded by this 'if' clause
352 | if(check) FREEMEMORY(space, check);
| ^~
Building... library for source build/match.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/match.o libs/match.c
Building... library for source build/charsequence.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/charsequence.o libs/charsequence.c
In file included from libs/charsequence.c:26:
libs/charsequence.c: In function 'destructSequence':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/charsequence.c:467:4: note: in expansion of macro 'FREEMEMORY'
467 | FREEMEMORY(space, sequence->sequence);
| ^~~~~~~~~~
libs/charsequence.c:466:3: note: some parts of macro expansion are not guarded by this 'if' clause
466 | if (sequence->sequence != NULL)
| ^~
In file included from libs/charsequence.c:26:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/charsequence.c:470:5: note: in expansion of macro 'FREEMEMORY'
470 | FREEMEMORY(space, sequence->alphabetname);
| ^~~~~~~~~~
libs/charsequence.c:469:2: note: some parts of macro expansion are not guarded by this 'if' clause
469 | if (sequence->alphabetname != NULL)
| ^~
In file included from libs/charsequence.c:26:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/charsequence.c:472:2: note: in expansion of macro 'FREEMEMORY'
472 | FREEMEMORY(space, sequence->url);
| ^~~~~~~~~~
libs/charsequence.c:471:5: note: some parts of macro expansion are not guarded by this 'if' clause
471 | if (sequence->url != NULL)
| ^~
In file included from libs/charsequence.c:26:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/charsequence.c:474:2: note: in expansion of macro 'FREEMEMORY'
474 | FREEMEMORY(space, sequence->info);
| ^~~~~~~~~~
libs/charsequence.c:473:5: note: some parts of macro expansion are not guarded by this 'if' clause
473 | if (sequence->info != NULL)
| ^~
Building... library for source build/stringutils.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/stringutils.o libs/stringutils.c
In file included from include/stringutils.h:27,
from libs/stringutils.c:39:
libs/stringutils.c: In function 'destructStringset':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/stringutils.c:274:9: note: in expansion of macro 'FREEMEMORY'
274 | FREEMEMORY(space, s->strings[i].str);
| ^~~~~~~~~~
libs/stringutils.c:273:7: note: some parts of macro expansion are not guarded by this 'if' clause
273 | if(s->strings[i].str != NULL)
| ^~
Building... library for source build/samio.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/samio.o libs/samio.c
Building... library for source build/manout.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/manout.o libs/manout.c
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from libs/samio.c:33:
libs/samio.c: In function 'bl_samDestructTag':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/samio.c:102:15: note: in expansion of macro 'FREEMEMORY'
102 | if(kv->tag) FREEMEMORY(NULL, kv->tag);
| ^~~~~~~~~~
libs/samio.c:102:3: note: some parts of macro expansion are not guarded by this 'if' clause
102 | if(kv->tag) FREEMEMORY(NULL, kv->tag);
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from libs/samio.c:33:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/samio.c:103:15: note: in expansion of macro 'FREEMEMORY'
103 | if(kv->val) FREEMEMORY(NULL, kv->val);
| ^~~~~~~~~~
libs/samio.c:103:3: note: some parts of macro expansion are not guarded by this 'if' clause
103 | if(kv->val) FREEMEMORY(NULL, kv->val);
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from libs/samio.c:33:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/samio.c:104:16: note: in expansion of macro 'FREEMEMORY'
104 | if(kv->type) FREEMEMORY(NULL, kv->type);
| ^~~~~~~~~~
libs/samio.c:104:3: note: some parts of macro expansion are not guarded by this 'if' clause
104 | if(kv->type) FREEMEMORY(NULL, kv->type);
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from libs/samio.c:33:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/samio.c:105:15: note: in expansion of macro 'FREEMEMORY'
105 | if(kv->key) FREEMEMORY(NULL, kv->key);
| ^~~~~~~~~~
libs/samio.c:105:3: note: some parts of macro expansion are not guarded by this 'if' clause
105 | if(kv->key) FREEMEMORY(NULL, kv->key);
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from libs/samio.c:33:
libs/samio.c: In function 'bl_samDestruct':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/samio.c:112:21: note: in expansion of macro 'FREEMEMORY'
112 | if(samrec->qname) FREEMEMORY(NULL, samrec->qname);
| ^~~~~~~~~~
libs/samio.c:112:3: note: some parts of macro expansion are not guarded by this 'if' clause
112 | if(samrec->qname) FREEMEMORY(NULL, samrec->qname);
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from libs/samio.c:33:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/samio.c:113:21: note: in expansion of macro 'FREEMEMORY'
113 | if(samrec->rname) FREEMEMORY(NULL, samrec->rname);
| ^~~~~~~~~~
libs/samio.c:113:3: note: some parts of macro expansion are not guarded by this 'if' clause
113 | if(samrec->rname) FREEMEMORY(NULL, samrec->rname);
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from libs/samio.c:33:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/samio.c:114:21: note: in expansion of macro 'FREEMEMORY'
114 | if(samrec->cigar) FREEMEMORY(NULL, samrec->cigar);
| ^~~~~~~~~~
libs/samio.c:114:3: note: some parts of macro expansion are not guarded by this 'if' clause
114 | if(samrec->cigar) FREEMEMORY(NULL, samrec->cigar);
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from libs/samio.c:33:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/samio.c:115:21: note: in expansion of macro 'FREEMEMORY'
115 | if(samrec->rnext) FREEMEMORY(NULL, samrec->rnext);
| ^~~~~~~~~~
libs/samio.c:115:3: note: some parts of macro expansion are not guarded by this 'if' clause
115 | if(samrec->rnext) FREEMEMORY(NULL, samrec->rnext);
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from libs/samio.c:33:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/samio.c:116:21: note: in expansion of macro 'FREEMEMORY'
116 | if(samrec->seq) FREEMEMORY(NULL, samrec->seq);
| ^~~~~~~~~~
libs/samio.c:116:3: note: some parts of macro expansion are not guarded by this 'if' clause
116 | if(samrec->seq) FREEMEMORY(NULL, samrec->seq);
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from libs/samio.c:33:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/samio.c:117:21: note: in expansion of macro 'FREEMEMORY'
117 | if(samrec->qual) FREEMEMORY(NULL, samrec->qual);
| ^~~~~~~~~~
libs/samio.c:117:3: note: some parts of macro expansion are not guarded by this 'if' clause
117 | if(samrec->qual) FREEMEMORY(NULL, samrec->qual);
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from libs/samio.c:33:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/samio.c:121:20: note: in expansion of macro 'FREEMEMORY'
121 | if(samrec->tags) FREEMEMORY(NULL, samrec->tags);
| ^~~~~~~~~~
libs/samio.c:121:3: note: some parts of macro expansion are not guarded by this 'if' clause
121 | if(samrec->tags) FREEMEMORY(NULL, samrec->tags);
| ^~
Building... library for source build/brendel.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/brendel.o libs/brendel.c
Building... library for source build/info.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/info.o libs/info.c
libs/info.c: In function 'timestr_r':
libs/info.c:64:50: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 12 [-Wformat-overflow=]
64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d",
| ^~
libs/info.c:64:21: note: directive argument in the range [-2147481748, 2147483647]
64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libs/info.c:64:5: note: 'sprintf' output between 16 and 67 bytes into a destination of size 26
64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
65 | wday_name[timeptr->tm_wday], mon_name[timeptr->tm_mon],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
66 | timeptr->tm_mday, timeptr->tm_hour, timeptr->tm_min,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
67 | timeptr->tm_sec, 1900 + timeptr->tm_year);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libs/info.c: In function 'infomsg':
libs/info.c:64:50: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 12 [-Wformat-overflow=]
64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d",
| ^~
libs/info.c:64:21: note: directive argument in the range [-2147481748, 2147483647]
64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libs/info.c:64:5: note: 'sprintf' output between 16 and 67 bytes into a destination of size 26
64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
65 | wday_name[timeptr->tm_wday], mon_name[timeptr->tm_mon],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
66 | timeptr->tm_mday, timeptr->tm_hour, timeptr->tm_min,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
67 | timeptr->tm_sec, 1900 + timeptr->tm_year);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libs/info.c: In function 'nfolevel':
libs/info.c:64:50: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 12 [-Wformat-overflow=]
64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d",
| ^~
libs/info.c:64:21: note: directive argument in the range [-2147481748, 2147483647]
64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libs/info.c:64:5: note: 'sprintf' output between 16 and 67 bytes into a destination of size 26
64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
65 | wday_name[timeptr->tm_wday], mon_name[timeptr->tm_mon],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
66 | timeptr->tm_mday, timeptr->tm_hour, timeptr->tm_min,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
67 | timeptr->tm_sec, 1900 + timeptr->tm_year);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libs/samio.c: In function 'bl_samgetNextSplitRefIdx':
libs/samio.c:369:3: warning: '%s' directive argument is null [-Wformat-overflow=]
369 | fprintf(stderr, "ref: '%s'\n", ref);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Building... library for source build/gzip.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/gzip.o libs/gzip.c
libs/gzip.c: In function 'readCommonHeader':
libs/gzip.c:41:56: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
41 | fprintf(stderr, "common header has a length of %ld instead of %ld - not good.\n", bytesRead, sizeof(u_CommonHeader));
| ~~^ ~~~~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
libs/gzip.c:41:71: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'unsigned int' [-Wformat=]
41 | fprintf(stderr, "common header has a length of %ld instead of %ld - not good.\n", bytesRead, sizeof(u_CommonHeader));
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~
| | |
| long int unsigned int
| %d
Building... library for source build/sufarray.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/sufarray.o libs/sufarray.c
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/sufarray.h:45,
from libs/sufarray.c:39:
libs/sufarray.c: In function 'destructSufArr':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/sufarray.c:613:5: note: in expansion of macro 'FREEMEMORY'
613 | FREEMEMORY(space, arr->lcpctab);
| ^~~~~~~~~~
libs/sufarray.c:612:3: note: some parts of macro expansion are not guarded by this 'if' clause
612 | if (arr->lcpctab != NULL)
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/sufarray.h:45,
from libs/sufarray.c:39:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/sufarray.c:615:5: note: in expansion of macro 'FREEMEMORY'
615 | FREEMEMORY(space, arr->inv_suftab);
| ^~~~~~~~~~
libs/sufarray.c:614:3: note: some parts of macro expansion are not guarded by this 'if' clause
614 | if (arr->inv_suftab != NULL)
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/sufarray.h:45,
from libs/sufarray.c:39:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/sufarray.c:619:5: note: in expansion of macro 'FREEMEMORY'
619 | FREEMEMORY(space, arr->idvtab);
| ^~~~~~~~~~
libs/sufarray.c:618:3: note: some parts of macro expansion are not guarded by this 'if' clause
618 | if (arr->idvtab != NULL)
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/sufarray.h:45,
from libs/sufarray.c:39:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/sufarray.c:624:5: note: in expansion of macro 'FREEMEMORY'
624 | FREEMEMORY(space, arr->suflink);
| ^~~~~~~~~~
libs/sufarray.c:620:3: note: some parts of macro expansion are not guarded by this 'if' clause
620 | if (arr->suflink != NULL)
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/sufarray.h:45,
from libs/sufarray.c:39:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/sufarray.c:627:5: note: in expansion of macro 'FREEMEMORY'
627 | FREEMEMORY(space, arr->chldtab);
| ^~~~~~~~~~
libs/sufarray.c:626:3: note: some parts of macro expansion are not guarded by this 'if' clause
626 | if (arr->chldtab != NULL)
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/sufarray.h:45,
from libs/sufarray.c:39:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/sufarray.c:629:5: note: in expansion of macro 'FREEMEMORY'
629 | FREEMEMORY(space, arr->mdfive);
| ^~~~~~~~~~
libs/sufarray.c:628:3: note: some parts of macro expansion are not guarded by this 'if' clause
628 | if (arr->mdfive)
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/sufarray.h:45,
from libs/sufarray.c:39:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/sufarray.c:631:5: note: in expansion of macro 'FREEMEMORY'
631 | FREEMEMORY(space, arr->llvtab);
| ^~~~~~~~~~
libs/sufarray.c:630:3: note: some parts of macro expansion are not guarded by this 'if' clause
630 | if(arr->llvtab != NULL)
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/sufarray.h:45,
from libs/sufarray.c:39:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/sufarray.c:636:5: note: in expansion of macro 'FREEMEMORY'
636 | FREEMEMORY(space, arr->id);
| ^~~~~~~~~~
libs/sufarray.c:632:3: note: some parts of macro expansion are not guarded by this 'if' clause
632 | if(arr->id != NULL)
| ^~
Building... library for source build/fileBins.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/fileBins.o libs/fileBins.c
Building... library for source build/splitalign.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/splitalign.o libs/splitalign.c
In file included from libs/fileBins.c:51:
libs/fileBins.c: In function 'bl_fileBinsSortLine':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/fileBins.c:901:18: note: in expansion of macro 'FREEMEMORY'
901 | if(fileSort) FREEMEMORY(space, line);
| ^~~~~~~~~~
libs/fileBins.c:901:5: note: some parts of macro expansion are not guarded by this 'if' clause
901 | if(fileSort) FREEMEMORY(space, line);
| ^~
In file included from include/stringutils.h:27,
from include/biofiles.h:43,
from include/alignment.h:38,
from include/bitvectoralg.h:32,
from include/splitalign.h:29,
from libs/splitalign.c:32:
libs/splitalign.c: In function 'bl_fixSplitAlignHoffmann':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/splitalign.c:1323:25: note: in expansion of macro 'FREEMEMORY'
1323 | if(leftseedno[0]) FREEMEMORY(space, leftseeds[0]);
| ^~~~~~~~~~
libs/splitalign.c:1323:7: note: some parts of macro expansion are not guarded by this 'if' clause
1323 | if(leftseedno[0]) FREEMEMORY(space, leftseeds[0]);
| ^~
In file included from include/stringutils.h:27,
from include/biofiles.h:43,
from include/alignment.h:38,
from include/bitvectoralg.h:32,
from include/splitalign.h:29,
from libs/splitalign.c:32:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/splitalign.c:1324:25: note: in expansion of macro 'FREEMEMORY'
1324 | if(leftseedno[1]) FREEMEMORY(space, leftseeds[1]);
| ^~~~~~~~~~
libs/splitalign.c:1324:7: note: some parts of macro expansion are not guarded by this 'if' clause
1324 | if(leftseedno[1]) FREEMEMORY(space, leftseeds[1]);
| ^~
In file included from include/stringutils.h:27,
from include/biofiles.h:43,
from include/alignment.h:38,
from include/bitvectoralg.h:32,
from include/splitalign.h:29,
from libs/splitalign.c:32:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/splitalign.c:1325:26: note: in expansion of macro 'FREEMEMORY'
1325 | if(rightseedno[0]) FREEMEMORY(space, rightseeds[0]);
| ^~~~~~~~~~
libs/splitalign.c:1325:7: note: some parts of macro expansion are not guarded by this 'if' clause
1325 | if(rightseedno[0]) FREEMEMORY(space, rightseeds[0]);
| ^~
In file included from include/stringutils.h:27,
from include/biofiles.h:43,
from include/alignment.h:38,
from include/bitvectoralg.h:32,
from include/splitalign.h:29,
from libs/splitalign.c:32:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/splitalign.c:1326:26: note: in expansion of macro 'FREEMEMORY'
1326 | if(rightseedno[1]) FREEMEMORY(space, rightseeds[1]);
| ^~~~~~~~~~
libs/splitalign.c:1326:7: note: some parts of macro expansion are not guarded by this 'if' clause
1326 | if(rightseedno[1]) FREEMEMORY(space, rightseeds[1]);
| ^~
In file included from include/stringutils.h:27,
from include/biofiles.h:43,
from include/alignment.h:38,
from include/bitvectoralg.h:32,
from include/splitalign.h:29,
from libs/splitalign.c:32:
libs/splitalign.c: In function 'bl_fixSplitAlignBrendel':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/splitalign.c:1565:27: note: in expansion of macro 'FREEMEMORY'
1565 | if(leftseedno[0]) FREEMEMORY(space, leftseeds[0]);
| ^~~~~~~~~~
libs/splitalign.c:1565:9: note: some parts of macro expansion are not guarded by this 'if' clause
1565 | if(leftseedno[0]) FREEMEMORY(space, leftseeds[0]);
| ^~
In file included from include/stringutils.h:27,
from include/biofiles.h:43,
from include/alignment.h:38,
from include/bitvectoralg.h:32,
from include/splitalign.h:29,
from libs/splitalign.c:32:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/splitalign.c:1566:27: note: in expansion of macro 'FREEMEMORY'
1566 | if(leftseedno[1]) FREEMEMORY(space, leftseeds[1]);
| ^~~~~~~~~~
libs/splitalign.c:1566:9: note: some parts of macro expansion are not guarded by this 'if' clause
1566 | if(leftseedno[1]) FREEMEMORY(space, leftseeds[1]);
| ^~
In file included from include/stringutils.h:27,
from include/biofiles.h:43,
from include/alignment.h:38,
from include/bitvectoralg.h:32,
from include/splitalign.h:29,
from libs/splitalign.c:32:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/splitalign.c:1567:28: note: in expansion of macro 'FREEMEMORY'
1567 | if(rightseedno[0]) FREEMEMORY(space, rightseeds[0]);
| ^~~~~~~~~~
libs/splitalign.c:1567:9: note: some parts of macro expansion are not guarded by this 'if' clause
1567 | if(rightseedno[0]) FREEMEMORY(space, rightseeds[0]);
| ^~
In file included from include/stringutils.h:27,
from include/biofiles.h:43,
from include/alignment.h:38,
from include/bitvectoralg.h:32,
from include/splitalign.h:29,
from libs/splitalign.c:32:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/splitalign.c:1568:28: note: in expansion of macro 'FREEMEMORY'
1568 | if(rightseedno[1]) FREEMEMORY(space, rightseeds[1]);
| ^~~~~~~~~~
libs/splitalign.c:1568:9: note: some parts of macro expansion are not guarded by this 'if' clause
1568 | if(rightseedno[1]) FREEMEMORY(space, rightseeds[1]);
| ^~
Building... library for source build/iupac.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/iupac.o libs/iupac.c
Building... library for source build/bitvectoralg.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/bitvectoralg.o libs/bitvectoralg.c
Building... library for source build/intervaltree.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/intervaltree.o libs/intervaltree.c
In file included from include/mathematics.h:117,
from libs/intervaltree.c:27:
libs/intervaltree.c: In function 'bl_intervaltreeDestruct':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/intervaltree.c:443:19: note: in expansion of macro 'FREEMEMORY'
443 | if(root->ncoll) FREEMEMORY(NULL, root->collisions);
| ^~~~~~~~~~
libs/intervaltree.c:443:3: note: some parts of macro expansion are not guarded by this 'if' clause
443 | if(root->ncoll) FREEMEMORY(NULL, root->collisions);
| ^~
Building... library for source build/haarz.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/haarz.o libs/haarz.c
Building... library for source build/manopt.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/manopt.o libs/manopt.c
Building... library for source build/mathematics.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/mathematics.o libs/mathematics.c
In file included from include/mathematics.h:117,
from libs/mathematics.c:38:
libs/mathematics.c: In function 'destructVector':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/mathematics.c:251:23: note: in expansion of macro 'FREEMEMORY'
251 | if (v->elements) FREEMEMORY(space, v->elements);
| ^~~~~~~~~~
libs/mathematics.c:251:6: note: some parts of macro expansion are not guarded by this 'if' clause
251 | if (v->elements) FREEMEMORY(space, v->elements);
| ^~
Building... library for source build/multicharseq.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/multicharseq.o libs/multicharseq.c
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from libs/multicharseq.c:38:
libs/multicharseq.c: In function 'destructMultiCharSeq':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/multicharseq.c:212:7: note: in expansion of macro 'FREEMEMORY'
212 | FREEMEMORY(space, mseq->markpos);
| ^~~~~~~~~~
libs/multicharseq.c:211:2: note: some parts of macro expansion are not guarded by this 'if' clause
211 | if (mseq->markpos != NULL)
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from libs/multicharseq.c:38:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/multicharseq.c:214:7: note: in expansion of macro 'FREEMEMORY'
214 | FREEMEMORY(space, mseq->map);
| ^~~~~~~~~~
libs/multicharseq.c:213:2: note: some parts of macro expansion are not guarded by this 'if' clause
213 | if (mseq->map != NULL)
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from libs/multicharseq.c:38:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/multicharseq.c:216:7: note: in expansion of macro 'FREEMEMORY'
216 | FREEMEMORY(space, mseq->ref);
| ^~~~~~~~~~
libs/multicharseq.c:215:5: note: some parts of macro expansion are not guarded by this 'if' clause
215 | if (mseq->ref != NULL)
| ^~
Building... library for source build/filebuffer.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/filebuffer.o libs/filebuffer.c
Building... library for source build/mapfrag.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/mapfrag.o libs/mapfrag.c
Building... library for source build/mappingqual.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/mappingqual.o libs/mappingqual.c
Building... library for source build/nw.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/nw.o libs/nw.c
Building... library for source build/alignment.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/alignment.o libs/alignment.c
Building... library for source build/matealign.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/matealign.o libs/matealign.c
In file included from include/mathematics.h:117,
from libs/alignment.c:38:
libs/alignment.c: In function 'wrapAlignment':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/alignment.c:97:18: note: in expansion of macro 'FREEMEMORY'
97 | if(al->rmvseq) FREEMEMORY(NULL, al->v);
| ^~~~~~~~~~
libs/alignment.c:97:3: note: some parts of macro expansion are not guarded by this 'if' clause
97 | if(al->rmvseq) FREEMEMORY(NULL, al->v);
| ^~
In file included from include/mathematics.h:117,
from libs/alignment.c:38:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/alignment.c:98:18: note: in expansion of macro 'FREEMEMORY'
98 | if(al->rmuseq) FREEMEMORY(NULL, al->u);
| ^~~~~~~~~~
libs/alignment.c:98:3: note: some parts of macro expansion are not guarded by this 'if' clause
98 | if(al->rmuseq) FREEMEMORY(NULL, al->u);
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/locus.h:41,
from include/mapfrag.h:39,
from libs/matealign.c:32:
libs/matealign.c: In function 'bl_matealign':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/matealign.c:313:15: note: in expansion of macro 'FREEMEMORY'
313 | if(npos[0]) FREEMEMORY(NULL, spos[0]);
| ^~~~~~~~~~
libs/matealign.c:313:3: note: some parts of macro expansion are not guarded by this 'if' clause
313 | if(npos[0]) FREEMEMORY(NULL, spos[0]);
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/locus.h:41,
from include/mapfrag.h:39,
from libs/matealign.c:32:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/matealign.c:314:15: note: in expansion of macro 'FREEMEMORY'
314 | if(npos[1]) FREEMEMORY(NULL, spos[1]);
| ^~~~~~~~~~
libs/matealign.c:314:3: note: some parts of macro expansion are not guarded by this 'if' clause
314 | if(npos[1]) FREEMEMORY(NULL, spos[1]);
| ^~
Linking segemehl
cc build/md5.o build/vstack.o build/queryalign.o build/annotation.o build/biofiles.o build/bitVector.o build/locus.o build/seqclip.o build/debug.o build/merge.o build/kdseed.o build/stack.o build/bamio.o build/vqueue.o build/aluruSort.o build/segemehl_helper.o build/bitArray.o build/samheader.o build/sw.o build/fileio.o build/kdchain.o build/vtprogressbar.o build/karlin.o build/bgzip.o build/gzidx.o build/portable_endian.o build/container.o build/bedfiles.o build/memory.o build/junctions.o build/pigeon.o build/radixsort.o build/sort.o build/match.o build/charsequence.o build/stringutils.o build/samio.o build/manout.o build/brendel.o build/info.o build/gzip.o build/sufarray.o build/fileBins.o build/splitalign.o build/iupac.o build/bitvectoralg.o build/intervaltree.o build/manopt.o build/mathematics.o build/multicharseq.o build/filebuffer.o build/mapfrag.o build/mappingqual.o build/nw.o build/alignment.o build/matealign.o build/segemehl.o -o ./segemehl.x -lm -lpthread -lz -lncurses -L libs -lform -lmenu -L/usr/local/lib/ `pkg-config --libs htslib` -Wl,-z,relro -Wl,-z,now
Linking haarz
cc build/md5.o build/vstack.o build/queryalign.o build/annotation.o build/biofiles.o build/bitVector.o build/locus.o build/seqclip.o build/debug.o build/merge.o build/kdseed.o build/stack.o build/bamio.o build/vqueue.o build/aluruSort.o build/segemehl_helper.o build/bitArray.o build/samheader.o build/sw.o build/fileio.o build/kdchain.o build/vtprogressbar.o build/karlin.o build/bgzip.o build/gzidx.o build/portable_endian.o build/container.o build/bedfiles.o build/memory.o build/junctions.o build/pigeon.o build/radixsort.o build/sort.o build/match.o build/charsequence.o build/stringutils.o build/samio.o build/manout.o build/brendel.o build/info.o build/gzip.o build/sufarray.o build/fileBins.o build/splitalign.o build/iupac.o build/bitvectoralg.o build/intervaltree.o build/manopt.o build/mathematics.o build/multicharseq.o build/filebuffer.o build/mapfrag.o build/mappingqual.o build/nw.o build/alignment.o build/matealign.o build/haarz.o -o ./haarz.x -lm -lpthread -lz -lncurses -L libs -lform -lmenu -L/usr/local/lib/ `pkg-config --libs htslib` -Wl,-z,relro -Wl,-z,now
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
mv segemehl.x segemehl
mv haarz.x haarz
find . -name "*.x"
dh_install
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
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
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/segemehl/usr/bin/segemehl debian/segemehl/usr/bin/haarz 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 'segemehl' in '../segemehl_0.3.4-3_armhf.deb'.
dpkg-deb: building package 'segemehl-dbgsym' in '../segemehl-dbgsym_0.3.4-3_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../segemehl_0.3.4-3_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2021-02-28T06:12:24Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
segemehl_0.3.4-3_armhf.changes:
-------------------------------
Format: 1.8
Date: Thu, 18 Feb 2021 15:14:26 +0530
Source: segemehl
Binary: segemehl segemehl-dbgsym
Architecture: armhf
Version: 0.3.4-3
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Nilesh Patra <npatra974@gmail.com>
Description:
segemehl - short read mapping with gaps
Changes:
segemehl (0.3.4-3) unstable; urgency=medium
.
* Team Upload.
* Do not hardcode pkg-config to fix
non cross-buildability
* d/u/metadata: Update URLs
Checksums-Sha1:
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e04a0a82aa0acf0d5fa41f5a9fc64dd7bedbcc79 5516 segemehl_0.3.4-3_armhf.buildinfo
2ec7b873bb437692e63e972e0ee29ec8172c3dae 221480 segemehl_0.3.4-3_armhf.deb
Checksums-Sha256:
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d1d333eb6bd2b38a4cb6939c452dd853f46d5d4d44e40eed9fff8dedc11ff379 5516 segemehl_0.3.4-3_armhf.buildinfo
bb109ecaab177794d05381fdce7cce949e98589bf290650a1ee2e478564ed638 221480 segemehl_0.3.4-3_armhf.deb
Files:
f37d2aa17eaca633c0853b619a12ac19 1375748 debug optional segemehl-dbgsym_0.3.4-3_armhf.deb
900cc2216dfd0d9786f14b4bab0a631f 5516 science optional segemehl_0.3.4-3_armhf.buildinfo
fb1b10c984c84227f564862fe8993561 221480 science optional segemehl_0.3.4-3_armhf.deb
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| Package contents |
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segemehl-dbgsym_0.3.4-3_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 1375748 bytes: control archive=644 bytes.
416 bytes, 12 lines control
300 bytes, 3 lines md5sums
Package: segemehl-dbgsym
Source: segemehl
Version: 0.3.4-3
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1499
Depends: segemehl (= 0.3.4-3)
Section: debug
Priority: optional
Description: debug symbols for segemehl
Build-Ids: 6860b1a2def9520a697b161c80326a2e949efb18 86409fc207c2eab935d62f4a526466e742d4c620
drwxr-xr-x root/root 0 2021-02-18 09:44 ./
drwxr-xr-x root/root 0 2021-02-18 09:44 ./usr/
drwxr-xr-x root/root 0 2021-02-18 09:44 ./usr/lib/
drwxr-xr-x root/root 0 2021-02-18 09:44 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-02-18 09:44 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-02-18 09:44 ./usr/lib/debug/.build-id/68/
-rw-r--r-- root/root 739584 2021-02-18 09:44 ./usr/lib/debug/.build-id/68/60b1a2def9520a697b161c80326a2e949efb18.debug
drwxr-xr-x root/root 0 2021-02-18 09:44 ./usr/lib/debug/.build-id/86/
-rw-r--r-- root/root 738900 2021-02-18 09:44 ./usr/lib/debug/.build-id/86/409fc207c2eab935d62f4a526466e742d4c620.debug
drwxr-xr-x root/root 0 2021-02-18 09:44 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2021-02-18 09:44 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 41372 2021-02-18 09:44 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/segemehl.debug
drwxr-xr-x root/root 0 2021-02-18 09:44 ./usr/share/
drwxr-xr-x root/root 0 2021-02-18 09:44 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-02-18 09:44 ./usr/share/doc/segemehl-dbgsym -> segemehl
segemehl_0.3.4-3_armhf.deb
--------------------------
new Debian package, version 2.0.
size 221480 bytes: control archive=1340 bytes.
1606 bytes, 29 lines control
374 bytes, 6 lines md5sums
Package: segemehl
Version: 0.3.4-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 989
Depends: libc6 (>= 2.29), libhts3 (>= 1.10), zlib1g (>= 1:1.2.2.4)
Section: science
Priority: optional
Homepage: http://www.bioinf.uni-leipzig.de/Software/segemehl/
Description: short read mapping with gaps
Segemehl is a software to map short sequencer reads to reference
genomes. Segemehl implements a matching strategy based on enhanced
suffix arrays (ESA). Segemehl accepts fasta and fastq queries (gzip'ed
and bgzip'ed). In addition to the alignment of reads from standard DNA-
and RNA-seq protocols, it also allows the mapping of bisulfite converted
reads (Lister and Cokus) and implements a split read mapping strategy.
The output of segemehl is a SAM or BAM formatted alignment file. In the
case of split-read mapping, additional BED files are written to the
disc. These BED files may be summarized with the postprocessing tool
haarz. In the case of the alignment of bisulfite converted reads, raw
methylation rates may also be called with haarz.
.
In brief, for each suffix of a read, segemehl aims to find the
best-scoring seed. Seeds might contain insertions, deletions, and
mismatches (differences). The number of differences allowed within a
single seed is user-controlled and is crucial for the runtime of the
program. Subsequently, seeds that undercut the user-defined E-value are
passed on to an exact semi-global alignment procedure. Finally, reads
with a minimum accuracy of percent are reported to the user.
drwxr-xr-x root/root 0 2021-02-18 09:44 ./
drwxr-xr-x root/root 0 2021-02-18 09:44 ./usr/
drwxr-xr-x root/root 0 2021-02-18 09:44 ./usr/bin/
-rwxr-xr-x root/root 493812 2021-02-18 09:44 ./usr/bin/haarz
-rwxr-xr-x root/root 502072 2021-02-18 09:44 ./usr/bin/segemehl
drwxr-xr-x root/root 0 2021-02-18 09:44 ./usr/share/
drwxr-xr-x root/root 0 2021-02-18 09:44 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-02-18 09:44 ./usr/share/doc/segemehl/
-rw-r--r-- root/root 448 2021-02-18 09:44 ./usr/share/doc/segemehl/changelog.Debian.gz
-rw-r--r-- root/root 1009 2021-02-18 09:25 ./usr/share/doc/segemehl/copyright
drwxr-xr-x root/root 0 2021-02-18 09:44 ./usr/share/man/
drwxr-xr-x root/root 0 2021-02-18 09:44 ./usr/share/man/man1/
-rw-r--r-- root/root 505 2021-02-18 09:44 ./usr/share/man/man1/haarz.1.gz
-rw-r--r-- root/root 2427 2021-02-18 09:44 ./usr/share/man/man1/segemehl.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: 14600
Build-Time: 32
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 261
Job: segemehl_0.3.4-3
Machine Architecture: armhf
Package: segemehl
Package-Time: 312
Source-Version: 0.3.4-3
Space: 14600
Status: successful
Version: 0.3.4-3
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Finished at 2021-02-28T06:12:24Z
Build needed 00:05:12, 14600k disk space