segemehl →
0.3.4-2 →
armhf → 2019-11-24 07:28:14
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| segemehl 0.3.4-2 (armhf) Sun, 24 Nov 2019 07:23:01 +0000 |
+==============================================================================+
Package: segemehl
Version: 0.3.4-2
Source Version: 0.3.4-2
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-f890cbe2-b90d-4e6a-94ef-36fc3afab5c9' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.5 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.9 MB]
Fetched 24.4 MB in 10s (2383 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 0.3.4-2 (dsc) [2005 B]
Get:2 http://172.17.0.1/private bullseye-staging/main segemehl 0.3.4-2 (tar) [244 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main segemehl 0.3.4-2 (diff) [5584 B]
Fetched 252 kB in 0s (507 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/segemehl-lw1EnY/segemehl-0.3.4' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/segemehl-lw1EnY' 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-yVuAGJ/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-yVuAGJ/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-yVuAGJ/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-yVuAGJ/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-yVuAGJ/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-yVuAGJ/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-yVuAGJ/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-yVuAGJ/apt_archive ./ Packages [428 B]
Fetched 2104 B in 0s (9301 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 24 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-yVuAGJ/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12227 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-yVuAGJ/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-yVuAGJ/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-yVuAGJ/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-yVuAGJ/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-yVuAGJ/apt_archive ./ Sources [521 B]
Get:5 copy:/<<BUILDDIR>>/resolver-yVuAGJ/apt_archive ./ Packages [597 B]
Fetched 2451 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 bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbrotli1 libbsd0 libcroco3
libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1
libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libhts-dev
libhts2 libicu63 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 libtinfo5 libtool libuchardet0 libxml2 m4 man-db
pkg-config po-debconf sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff 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 bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbrotli1 libbsd0 libcroco3
libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1
libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libhts-dev
libhts2 libicu63 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 libtinfo5 libtool libuchardet0 libxml2 m4 man-db
pkg-config po-debconf sbuild-build-depends-segemehl-dummy sensible-utils
zlib1g-dev
0 upgraded, 56 newly installed, 0 to remove and 24 not upgraded.
Need to get 26.9 MB of archives.
After this operation, 83.6 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-yVuAGJ/apt_archive ./ sbuild-build-depends-segemehl-dummy 0.invalid.0 [892 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.1+20191019-1 [316 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-3 [782 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.1-2 [26.6 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.0-1 [1261 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12 [15.8 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.37-6 [253 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.37-6 [111 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.37-6 [66.2 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-11 [547 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.67-1 [104 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.6.1-1 [23.5 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.6.1-1 [14.4 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-2 [136 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 12.7.1 [173 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.62.2-3 [1137 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-8 [593 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.1+20191019-1 [79.5 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.7.1 [997 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.7-5 [257 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6-6 [14.0 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-6+b1 [61.5 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-6+b1 [112 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1d-2 [1268 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-6+b1 [316 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-6+b1 [134 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.39.2-1 [71.3 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b1 [54.3 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.66.0-1+b1 [295 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.3-3 [76.4 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libhts2 armhf 1.9-11 [255 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libhts-dev armhf 1.9-11 [4286 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libncurses-dev armhf 6.1+20191019-1 [284 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf pkg-config armhf 0.29-6 [59.8 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking libkrb5support0:armhf (1.17-6+b1) ...
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Unpacking sbuild-build-depends-segemehl-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.5.1-2) ...
Setting up libkeyutils1:armhf (1.6-6) ...
Setting up libpsl5:armhf (0.20.2-2) ...
Setting up libmagic-mgc (1:5.37-6) ...
Setting up libarchive-zip-perl (1.67-1) ...
Setting up libglib2.0-0:armhf (2.62.2-3) ...
No schema files found: doing nothing.
Setting up libssl1.1:armhf (1.1.1d-2) ...
Setting up libdebhelper-perl (12.7.1) ...
Setting up libbrotli1:armhf (1.0.7-5) ...
Setting up libnghttp2-14:armhf (1.39.2-1) ...
Setting up libmagic1:armhf (1:5.37-6) ...
Setting up libdeflate0 (1.3-3) ...
Setting up gettext-base (0.19.8.1-9) ...
Setting up file (1:5.37-6) ...
Setting up libicu63:armhf (63.2-2) ...
Setting up libkrb5support0:armhf (1.17-6+b1) ...
Setting up autotools-dev (20180224.1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b1) ...
Setting up libncurses6:armhf (6.1+20191019-1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up autopoint (0.19.8.1-9) ...
Setting up pkg-config (0.29-6) ...
Setting up libk5crypto3:armhf (1.17-6+b1) ...
Setting up liblzma-dev:armhf (5.2.4-1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up sensible-utils (0.0.12) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.8.0-2.1) ...
Setting up libkrb5-3:armhf (1.17-6+b1) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libtinfo5:armhf (6.1+20191019-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-8) ...
Setting up libfile-stripnondeterminism-perl (1.6.1-1) ...
Setting up libncurses-dev:armhf (6.1+20191019-1) ...
Setting up libtool (2.4.6-11) ...
Setting up m4 (1.4.18-4) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libgssapi-krb5-2:armhf (1.17-6+b1) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up autoconf (2.69-11) ...
Setting up dwz (0.13-2) ...
Setting up groff-base (1.22.4-3) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up gettext (0.19.8.1-9) ...
Setting up libcurl3-gnutls:armhf (7.66.0-1+b1) ...
Setting up man-db (2.9.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libhts2:armhf (1.9-11) ...
Setting up po-debconf (1.0.21) ...
Setting up libhts-dev:armhf (1.9-11) ...
Setting up debhelper (12.7.1) ...
Setting up dh-autoreconf (19) ...
Setting up dh-strip-nondeterminism (1.6.1-1) ...
Setting up sbuild-build-depends-segemehl-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.29-2+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-58-generic armhf (armv8l)
Toolchain package versions: binutils_2.33.1-2+rpi1 dpkg-dev_1.19.7 g++-9_9.2.1-17+rpi1 gcc-9_9.2.1-17+rpi1 libc6-dev_2.29-2+rpi1 libstdc++-9-dev_9.2.1-17+rpi1 libstdc++6_9.2.1-17+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.46 bash_5.0-5 binutils_2.33.1-2+rpi1 binutils-arm-linux-gnueabihf_2.33.1-2+rpi1 binutils-common_2.33.1-2+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3 cpp_4:9.2.1-3+rpi1 cpp-9_9.2.1-17+rpi1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.7.1 debianutils_4.9 dh-autoreconf_19 dh-strip-nondeterminism_1.6.1-1 diffutils_1:3.7-3 dirmngr_2.2.17-3+b1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-2 e2fsprogs_1.45.4-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.37-6 findutils_4.7.0-1 g++_4:9.2.1-3+rpi1 g++-9_9.2.1-17+rpi1 gcc_4:9.2.1-3+rpi1 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-6-base_6.5.0-1+rpi1+b3 gcc-9_9.2.1-17+rpi1 gcc-9-base_9.2.1-17+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gnupg_2.2.17-3 gnupg-l10n_2.2.17-3 gnupg-utils_2.2.17-3+b1 gpg_2.2.17-3+b1 gpg-agent_2.2.17-3+b1 gpg-wks-client_2.2.17-3+b1 gpg-wks-server_2.2.17-3+b1 gpgconf_2.2.17-3+b1 gpgsm_2.2.17-3+b1 gpgv_2.2.17-3+b1 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-2 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-17+rpi1 libassuan0_2.5.3-7 libatomic1_9.2.1-17+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2 libbinutils_2.33.1-2+rpi1 libblkid1_2.34-0.1 libbrotli1_1.0.7-5 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-2+rpi1 libc-dev-bin_2.29-2+rpi1 libc6_2.29-2+rpi1 libc6-dev_2.29-2+rpi1 libcap-ng0_0.7.9-2.1 libcap2_1:2.27-1 libcap2-bin_1:2.27-1 libcc1-0_9.2.1-17+rpi1 libcom-err2_1.45.4-1 libcroco3_0.6.13-1 libcurl3-gnutls_7.66.0-1+b1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.250 libdebhelper-perl_12.7.1 libdeflate0_1.3-3 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libext2fs2_1.45.4-1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.6.1-1 libgcc-9-dev_9.2.1-17+rpi1 libgcc1_1:9.2.1-17+rpi1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.62.2-3 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.10-4 libgomp1_9.2.1-17+rpi1 libgpg-error0_1.36-7 libgssapi-krb5-2_1.17-6+b1 libhogweed5_3.5.1+really3.5.1-2 libhts-dev_1.9-11 libhts2_1.9-11 libicu63_63.2-2 libidn2-0_2.2.0-2 libisl19_0.20-2 libisl21_0.21-2 libk5crypto3_1.17-6+b1 libkeyutils1_1.6-6 libkrb5-3_1.17-6+b1 libkrb5support0_1.17-6+b1 libksba8_1.3.5-2 libldap-2.4-2_2.4.48+dfsg-1+b2 libldap-common_2.4.48+dfsg-1 liblz4-1_1.9.2-1 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-6 libmagic1_1:5.37-6 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncurses-dev_6.1+20191019-1 libncurses6_6.1+20191019-1 libncursesw6_6.1+20191019-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.39.2-1 libnpth0_1.6-1 libp11-kit0_0.23.18.1-2 libpam-cap_1:2.27-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.32-5 libpcre3_2:8.39-12 libperl5.30_5.30.0-9 libpipeline1_1.5.1-2 libpsl5_0.20.2-2 libreadline7_7.0-5 libreadline8_8.0-3 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 libsasl2-2_2.1.27+dfsg-1+b1 libsasl2-modules-db_2.1.27+dfsg-1+b1 libseccomp2_2.4.1-2+rpi1 libselinux1_2.9-2 libsemanage-common_2.9-3 libsemanage1_2.9-3 libsepol1_2.9-2 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.30.1-1 libss2_1.45.4-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1d-2 libstdc++-9-dev_9.2.1-17+rpi1 libstdc++6_9.2.1-17+rpi1 libsub-override-perl_0.09-2 libsystemd0_242-7+rpi1 libtasn1-6_4.14-3 libtinfo5_6.1+20191019-1 libtinfo6_6.1+20191019-1 libtool_2.4.6-11 libubsan1_9.2.1-17+rpi1 libuchardet0_0.0.6-3 libudev1_242-7+rpi1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml2_2.9.4+dfsg1-8 libzstd1_1.4.3+dfsg-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.7-2 logsave_1.45.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-1 mawk_1.3.3-17 mount_2.34-0.1 ncurses-base_6.1+20191019-1 ncurses-bin_6.1+20191019-1 netbase_5.6 passwd_1:4.7-2 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 pkg-config_0.29-6 po-debconf_1.0.21 raspbian-archive-keyring_20120528.2 readline-common_8.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-segemehl-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.96-1 tar_1.30+dfsg-6 tzdata_2019c-3 util-linux_2.34-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Mon Nov 18 22:03:27 2019 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./segemehl_0.3.4-2.dsc
dpkg-source: info: extracting segemehl in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking segemehl_0.3.4.orig.tar.xz
dpkg-source: info: unpacking segemehl_0.3.4-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying rpath.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-f890cbe2-b90d-4e6a-94ef-36fc3afab5c9
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package segemehl
dpkg-buildpackage: info: source version 0.3.4-2
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 -fdebug-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
cc -g -O2 -fdebug-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
Building... library for source build/annotation.o
cc -g -O2 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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
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/sort.o
cc -g -O2 -fdebug-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
Building... library for source build/match.o
cc -g -O2 -fdebug-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 -fdebug-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 -fdebug-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
Building... library for source build/samio.o
cc -g -O2 -fdebug-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
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/manout.o
cc -g -O2 -fdebug-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 -fdebug-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 -fdebug-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/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Building... library for source build/gzip.o
cc -g -O2 -fdebug-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 -fdebug-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
Building... library for source build/fileBins.o
cc -g -O2 -fdebug-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 -fdebug-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 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);
| ^~~~~~~~~~
In file included from libs/fileBins.c:51:
libs/fileBins.c: In function 'bl_fileBinsSortLine':
libs/sufarray.c:614:3: note: some parts of macro expansion are not guarded by this 'if' clause
614 | if (arr->inv_suftab != NULL)
| ^~
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/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)
| ^~
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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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
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);
| ^~
Building... library for source build/matealign.o
cc -g -O2 -fdebug-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/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
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/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
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/haarz debian/segemehl/usr/bin/segemehl 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_0.3.4-2_armhf.deb'.
dpkg-deb: building package 'segemehl-dbgsym' in '../segemehl-dbgsym_0.3.4-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../segemehl_0.3.4-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2019-11-24T07:28:11Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
segemehl_0.3.4-2_armhf.changes:
-------------------------------
Format: 1.8
Date: Mon, 18 Nov 2019 22:59:53 +0100
Source: segemehl
Binary: segemehl segemehl-dbgsym
Architecture: armhf
Version: 0.3.4-2
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
segemehl - short read mapping with gaps
Closes: 945040
Changes:
segemehl (0.3.4-2) unstable; urgency=medium
.
* Fix typo in long description
Closes: #945040
* debhelper-compat 12
* Standards-Version: 4.4.1
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Checksums-Sha256:
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Files:
88c686bcb2cdb0cd0362602c4d0910e1 1368500 debug optional segemehl-dbgsym_0.3.4-2_armhf.deb
207b24d17c2dfd8bfa0215af50e43101 5401 science optional segemehl_0.3.4-2_armhf.buildinfo
a4504b9da6e979005346988fcc8eb735 225184 science optional segemehl_0.3.4-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
segemehl-dbgsym_0.3.4-2_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 1368500 bytes: control archive=644 bytes.
416 bytes, 12 lines control
300 bytes, 3 lines md5sums
Package: segemehl-dbgsym
Source: segemehl
Version: 0.3.4-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1499
Depends: segemehl (= 0.3.4-2)
Section: debug
Priority: optional
Description: debug symbols for segemehl
Build-Ids: 2d84b5b6ca4d3c404b6ce3123ab9bb53d38ca1a4 c5d16f4a766590ab39cafe8a2a7c4ac339776d10
drwxr-xr-x root/root 0 2019-11-18 21:59 ./
drwxr-xr-x root/root 0 2019-11-18 21:59 ./usr/
drwxr-xr-x root/root 0 2019-11-18 21:59 ./usr/lib/
drwxr-xr-x root/root 0 2019-11-18 21:59 ./usr/lib/debug/
drwxr-xr-x root/root 0 2019-11-18 21:59 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2019-11-18 21:59 ./usr/lib/debug/.build-id/2d/
-rw-r--r-- root/root 739756 2019-11-18 21:59 ./usr/lib/debug/.build-id/2d/84b5b6ca4d3c404b6ce3123ab9bb53d38ca1a4.debug
drwxr-xr-x root/root 0 2019-11-18 21:59 ./usr/lib/debug/.build-id/c5/
-rw-r--r-- root/root 740108 2019-11-18 21:59 ./usr/lib/debug/.build-id/c5/d16f4a766590ab39cafe8a2a7c4ac339776d10.debug
drwxr-xr-x root/root 0 2019-11-18 21:59 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2019-11-18 21:59 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 40844 2019-11-18 21:59 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/segemehl.debug
drwxr-xr-x root/root 0 2019-11-18 21:59 ./usr/share/
drwxr-xr-x root/root 0 2019-11-18 21:59 ./usr/share/doc/
lrwxrwxrwx root/root 0 2019-11-18 21:59 ./usr/share/doc/segemehl-dbgsym -> segemehl
segemehl_0.3.4-2_armhf.deb
--------------------------
new Debian package, version 2.0.
size 225184 bytes: control archive=1340 bytes.
1608 bytes, 29 lines control
374 bytes, 6 lines md5sums
Package: segemehl
Version: 0.3.4-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1001
Depends: libc6 (>= 2.29), libhts2 (>= 1.4.1), 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 2019-11-18 21:59 ./
drwxr-xr-x root/root 0 2019-11-18 21:59 ./usr/
drwxr-xr-x root/root 0 2019-11-18 21:59 ./usr/bin/
-rwxr-xr-x root/root 502004 2019-11-18 21:59 ./usr/bin/haarz
-rwxr-xr-x root/root 506168 2019-11-18 21:59 ./usr/bin/segemehl
drwxr-xr-x root/root 0 2019-11-18 21:59 ./usr/share/
drwxr-xr-x root/root 0 2019-11-18 21:59 ./usr/share/doc/
drwxr-xr-x root/root 0 2019-11-18 21:59 ./usr/share/doc/segemehl/
-rw-r--r-- root/root 327 2019-11-18 21:59 ./usr/share/doc/segemehl/changelog.Debian.gz
-rw-r--r-- root/root 1009 2019-11-18 21:59 ./usr/share/doc/segemehl/copyright
drwxr-xr-x root/root 0 2019-11-18 21:59 ./usr/share/man/
drwxr-xr-x root/root 0 2019-11-18 21:59 ./usr/share/man/man1/
-rw-r--r-- root/root 505 2019-11-18 21:59 ./usr/share/man/man1/haarz.1.gz
-rw-r--r-- root/root 2427 2019-11-18 21:59 ./usr/share/man/man1/segemehl.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 14700
Build-Time: 34
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 259
Job: segemehl_0.3.4-2
Machine Architecture: armhf
Package: segemehl
Package-Time: 310
Source-Version: 0.3.4-2
Space: 14700
Status: successful
Version: 0.3.4-2
--------------------------------------------------------------------------------
Finished at 2019-11-24T07:28:11Z
Build needed 00:05:10, 14700k disk space