segemehl →
0.3.4-5 →
armhf → 2021-08-27 11:29:15
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testbuildd
+==============================================================================+
| segemehl 0.3.4-5 (armhf) Fri, 27 Aug 2021 11:21:47 +0000 |
+==============================================================================+
Package: segemehl
Version: 0.3.4-5
Source Version: 0.3.4-5
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-37e731fb-e55b-4c8a-91bc-25ef8bed4de9' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bookworm-staging/main Sources [12.3 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.3 MB]
Fetched 25.6 MB in 29s (876 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 254 kB of source archives.
Get:1 http://172.17.0.1/private bookworm-staging/main segemehl 0.3.4-5 (dsc) [2032 B]
Get:2 http://172.17.0.1/private bookworm-staging/main segemehl 0.3.4-5 (tar) [244 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main segemehl 0.3.4-5 (diff) [7788 B]
Fetched 254 kB in 1s (451 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/segemehl-ZJQE6n/segemehl-0.3.4' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/segemehl-ZJQE6n' 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-cZJ7sf/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-cZJ7sf/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-cZJ7sf/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-cZJ7sf/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-cZJ7sf/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-cZJ7sf/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-cZJ7sf/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-cZJ7sf/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (2940 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 30 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-cZJ7sf/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (22.1 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12488 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 (= 13), pkg-config, libhts-dev, libncurses-dev, zlib1g-dev
Filtered Build-Depends: debhelper-compat (= 13), pkg-config, libhts-dev, libncurses-dev, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-segemehl-dummy' in '/<<BUILDDIR>>/resolver-cZJ7sf/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-cZJ7sf/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-cZJ7sf/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-cZJ7sf/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-cZJ7sf/apt_archive ./ Sources [524 B]
Get:5 copy:/<<BUILDDIR>>/resolver-cZJ7sf/apt_archive ./ Packages [600 B]
Fetched 2457 B in 1s (3397 B/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 package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbrotli1 libcurl3-gnutls
libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1
libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts3 libicu67
liblzma-dev libmagic-mgc libmagic1 libncurses-dev libncurses6 libnghttp2-14
libpipeline1 libpsl5 librtmp1 libsigsegv2 libssh2-1 libsub-override-perl
libtool libuchardet0 libxml2 m4 man-db pkg-config po-debconf sensible-utils
zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff libcurl4-doc libgnutls28-dev
libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev 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 libgpm2 publicsuffix libltdl-dev
libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbrotli1 libcurl3-gnutls
libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1
libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts3 libicu67
liblzma-dev libmagic-mgc libmagic1 libncurses-dev libncurses6 libnghttp2-14
libpipeline1 libpsl5 librtmp1 libsigsegv2 libssh2-1 libsub-override-perl
libtool libuchardet0 libxml2 m4 man-db pkg-config po-debconf
sbuild-build-depends-segemehl-dummy sensible-utils zlib1g-dev
0 upgraded, 49 newly installed, 0 to remove and 30 not upgraded.
Need to get 25.0 MB of archives.
After this operation, 80.7 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-cZJ7sf/apt_archive ./ sbuild-build-depends-segemehl-dummy 0.invalid.0 [888 B]
Get:2 http://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-1 [135 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.0.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-6 [793 kB]
Get:5 http://172.17.0.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:6 http://172.17.0.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:7 http://172.17.0.1/private bookworm-staging/main armhf sensible-utils all 0.0.14 [14.8 kB]
Get:8 http://172.17.0.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:9 http://172.17.0.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:10 http://172.17.0.1/private bookworm-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:11 http://172.17.0.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:12 http://172.17.0.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:13 http://172.17.0.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:14 http://172.17.0.1/private bookworm-staging/main armhf autoconf all 2.69-14 [313 kB]
Get:15 http://172.17.0.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:16 http://172.17.0.1/private bookworm-staging/main armhf automake all 1:1.16.3-2 [814 kB]
Get:17 http://172.17.0.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:18 http://172.17.0.1/private bookworm-staging/main armhf libdebhelper-perl all 13.4.1 [191 kB]
Get:19 http://172.17.0.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:20 http://172.17.0.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:21 http://172.17.0.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:22 http://172.17.0.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:23 http://172.17.0.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB]
Get:24 http://172.17.0.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB]
Get:25 http://172.17.0.1/private bookworm-staging/main armhf libelf1 armhf 0.185-2 [168 kB]
Get:26 http://172.17.0.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:27 http://172.17.0.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:28 http://172.17.0.1/private bookworm-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.7 [580 kB]
Get:29 http://172.17.0.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:30 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.4.1 [1039 kB]
Get:33 http://172.17.0.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:34 http://172.17.0.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.43.0-1 [65.3 kB]
Get:35 http://172.17.0.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:36 http://172.17.0.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:37 http://172.17.0.1/private bookworm-staging/main armhf libssh2-1 armhf 1.9.0-3 [151 kB]
Get:38 http://172.17.0.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.74.0-1.3 [301 kB]
Get:39 http://172.17.0.1/private bookworm-staging/main armhf libcurl4-gnutls-dev armhf 7.74.0-1.3 [375 kB]
Get:40 http://172.17.0.1/private bookworm-staging/main armhf libdeflate0 armhf 1.7-2 [44.1 kB]
Get:41 http://172.17.0.1/private bookworm-staging/main armhf libdeflate-dev armhf 1.7-2 [40.5 kB]
Get:42 http://172.17.0.1/private bookworm-staging/main armhf libglib2.0-0 armhf 2.68.4-1 [1197 kB]
Get:43 http://172.17.0.1/private bookworm-staging/main armhf libhts3 armhf 1.11-4 [324 kB]
Get:44 http://172.17.0.1/private bookworm-staging/main armhf liblzma-dev armhf 5.2.5-2 [219 kB]
Get:45 http://172.17.0.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:46 http://172.17.0.1/private bookworm-staging/main armhf libhts-dev armhf 1.11-4 [3815 kB]
Get:47 http://172.17.0.1/private bookworm-staging/main armhf libncurses6 armhf 6.2+20201114-2 [79.9 kB]
Get:48 http://172.17.0.1/private bookworm-staging/main armhf libncurses-dev armhf 6.2+20201114-2 [288 kB]
Get:49 http://172.17.0.1/private bookworm-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
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Unpacking libhts-dev:armhf (1.11-4) ...
Selecting previously unselected package libncurses6:armhf.
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Unpacking libncurses6:armhf (6.2+20201114-2) ...
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Unpacking libncurses-dev:armhf (6.2+20201114-2) ...
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Preparing to unpack .../47-pkg-config_0.29.2-1_armhf.deb ...
Unpacking pkg-config (0.29.2-1) ...
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Preparing to unpack .../48-sbuild-build-depends-segemehl-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-segemehl-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up libpsl5:armhf (0.21.0-1.2) ...
Setting up bsdextrautils (2.37.2-1) ...
update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
Setting up libicu67:armhf (67.1-7) ...
Setting up libmagic-mgc (1:5.39-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.68.4-1) ...
No schema files found: doing nothing.
Setting up libdebhelper-perl (13.4.1) ...
Setting up libbrotli1:armhf (1.0.9-2+b1) ...
Setting up libnghttp2-14:armhf (1.43.0-1) ...
Setting up libmagic1:armhf (1:5.39-3) ...
Setting up libdeflate0:armhf (1.7-2) ...
Setting up gettext-base (0.21-4) ...
Setting up file (1:5.39-3) ...
Setting up autotools-dev (20180224.1+nmu1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libncurses6:armhf (6.2+20201114-2) ...
Setting up libsigsegv2:armhf (2.13-1) ...
Setting up autopoint (0.21-4) ...
Setting up pkg-config (0.29.2-1) ...
Setting up liblzma-dev:armhf (5.2.5-2) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up sensible-utils (0.0.14) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.9.0-3) ...
Setting up libdeflate-dev:armhf (1.7-2) ...
Setting up libelf1:armhf (0.185-2) ...
Setting up libxml2:armhf (2.9.10+dfsg-6.7) ...
Setting up libfile-stripnondeterminism-perl (1.12.0-1) ...
Setting up libncurses-dev:armhf (6.2+20201114-2) ...
Setting up gettext (0.21-4) ...
Setting up libtool (2.4.6-15) ...
Setting up m4 (1.4.18-5) ...
Setting up libcurl3-gnutls:armhf (7.74.0-1.3) ...
Setting up libcurl4-gnutls-dev:armhf (7.74.0-1.3) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up autoconf (2.69-14) ...
Setting up dh-strip-nondeterminism (1.12.0-1) ...
Setting up dwz (0.14-1) ...
Setting up groff-base (1.22.4-6) ...
Setting up automake (1:1.16.3-2) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libhts3:armhf (1.11-4) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libhts-dev:armhf (1.11-4) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up dh-autoreconf (20) ...
Setting up debhelper (13.4.1) ...
Setting up sbuild-build-depends-segemehl-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-13+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.35.2-2+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.2.1-6+rpi1 gcc-10_10.2.1-6+rpi1 libc6-dev_2.31-13+rpi1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 linux-libc-dev_5.10.46-4+rpi1
Package versions: adduser_3.118 apt_2.2.4 autoconf_2.69-14 automake_1:1.16.3-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_11.1+rpi1 base-passwd_3.5.51 bash_5.1-2 binutils_2.35.2-2+rpi1 binutils-arm-linux-gnueabihf_2.35.2-2+rpi1 binutils-common_2.35.2-2+rpi1 bsdextrautils_2.37.2-1 bsdutils_1:2.36.1-8 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.2.1-6+rpi1 dash_0.5.11+git20200708+dd9ef66-5 debconf_1.5.77 debhelper_13.4.1 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.2-2 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.2.1-6+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.2.1-6+rpi1 gcc-10-base_10.2.1-6+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.3.0-22+rpi1 gettext_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.6-1 groff-base_1.22.4-6 gzip_1.10-4 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-10 libapt-pkg6.0_2.2.4 libarchive-zip-perl_1.68-1 libasan6_10.2.1-6+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.1-6+rpi1 libattr1_1:2.4.48-6 libaudit-common_1:3.0-2 libaudit1_1:3.0-2 libbinutils_2.35.2-2+rpi1 libblkid1_2.36.1-8 libbrotli1_1.0.9-2+b1 libbz2-1.0_1.0.8-4 libc-bin_2.31-13+rpi1 libc-dev-bin_2.31-13+rpi1 libc6_2.31-13+rpi1 libc6-dev_2.31-13+rpi1 libcap-ng0_0.7.9-2.2+b1 libcc1-0_10.2.1-6+rpi1 libcom-err2_1.46.2-2 libcrypt-dev_1:4.4.18-4 libcrypt1_1:4.4.18-4 libctf-nobfd0_2.35.2-2+rpi1 libctf0_2.35.2-2+rpi1 libcurl3-gnutls_7.74.0-1.3 libcurl4-gnutls-dev_7.74.0-1.3 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.4.1 libdeflate-dev_1.7-2 libdeflate0_1.7-2 libdpkg-perl_1.20.9+rpi1 libelf1_0.185-2 libext2fs2_1.46.2-2 libfakeroot_1.25.3-1.1 libffi7_3.3-6 libfile-stripnondeterminism-perl_1.12.0-1 libgcc-10-dev_10.2.1-6+rpi1 libgcc-s1_10.2.1-6+rpi1 libgcrypt20_1.8.7-6 libgdbm-compat4_1.19-2 libgdbm6_1.19-2 libglib2.0-0_2.68.4-1 libgmp10_2:6.2.1+dfsg-1 libgnutls30_3.7.1-5 libgomp1_10.2.1-6+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.18.3-6 libhogweed6_3.7.3-1 libhts-dev_1.11-4 libhts3_1.11-4 libicu67_67.1-7 libidn2-0_2.3.0-5 libisl23_0.23-1 libk5crypto3_1.18.3-6 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-6 libkrb5support0_1.18.3-6 libksba8_1.5.0-3 libldap-2.4-2_2.4.57+dfsg-3 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.3-2 liblzma-dev_5.2.5-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.36.1-8 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncurses-dev_6.2+20201114-2 libncurses6_6.2+20201114-2 libncursesw6_6.2+20201114-2 libnettle8_3.7.3-1 libnghttp2-14_1.43.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.23.22-1 libpam-modules_1.4.0-9 libpam-modules-bin_1.4.0-9 libpam-runtime_1.4.0-9 libpam0g_1.4.0-9 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-4+deb11u1 libpipeline1_1.5.3-1 libpsl5_0.21.0-1.2 libreadline8_8.1-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.36.1-8 libsqlite3-0_3.34.1-3 libss2_1.46.2-2 libssh2-1_1.9.0-3 libssl1.1_1.1.1k-1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.3-6+rpi1 libtasn1-6_4.16.0-2 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.2+20201114-2 libtirpc-common_1.3.1-1 libtirpc-dev_1.3.1-1 libtirpc3_1.3.1-1 libtool_2.4.6-15 libubsan1_10.2.1-6+rpi1 libuchardet0_0.0.7-1 libudev1_247.3-6+rpi1 libunistring2_0.9.10-4 libuuid1_2.36.1-8 libxml2_2.9.10+dfsg-6.7 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-2.1+rpi1 linux-libc-dev_5.10.46-4+rpi1 login_1:4.8.1-1 logsave_1.46.2-2 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 mount_2.36.1-8 ncurses-base_6.2+20201114-2 ncurses-bin_6.2+20201114-2 netbase_6.3 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-4+deb11u1 perl-base_5.32.1-4+deb11u1 perl-modules-5.32_5.32.1-5 pinentry-curses_1.1.0-4 pkg-config_0.29.2-1 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-segemehl-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.14 sysvinit-utils_2.96-7 tar_1.34+dfsg-1 tzdata_2021a-1 util-linux_2.36.1-8 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.LnpLWmFY/trustedkeys.kbx': General error
gpgv: Signature made Tue Aug 24 16:51:21 2021 UTC
gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
gpgv: issuer "npatra974@gmail.com"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./segemehl_0.3.4-5.dsc
dpkg-source: info: extracting segemehl in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking segemehl_0.3.4.orig.tar.xz
dpkg-source: info: unpacking segemehl_0.3.4-5.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying rpath.patch
dpkg-source: info: applying cross.patch
dpkg-source: info: applying arm64.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-37e731fb-e55b-4c8a-91bc-25ef8bed4de9
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package segemehl
dpkg-buildpackage: info: source version 0.3.4-5
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
dh_auto_clean
make -j4 clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Cleaning...
rm -f -r build segemehl haarz
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build -- all
make -j4 "INSTALL=install --strip-program=true" all
make[2]: Entering directory '/<<PKGBUILDDIR>>'
Building... library for source build/md5.o
Building... library for source build/vstack.o
Building... library for source build/queryalign.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/md5.o libs/md5.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/vstack.o libs/vstack.c
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/queryalign.o libs/queryalign.c
Building... library for source build/annotation.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/annotation.o libs/annotation.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) ;
| ^~
Building... library for source build/bitVector.o
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) ;
| ^~
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/bitVector.o libs/bitVector.c
Building... library for source build/locus.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/locus.o libs/locus.c
Building... library for source build/seqclip.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/seqclip.o libs/seqclip.c
Building... library for source build/debug.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/debug.o libs/debug.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/kdseed.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/kdseed.o libs/kdseed.c
Building... library for source build/stack.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/stack.o libs/stack.c
Building... library for source build/bamio.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/bamio.o libs/bamio.c
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from include/bamio.h:21,
from libs/bamio.c:32:
libs/bamio.c: In function 'bl_bamCrossSectionDestruct':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/bamio.c:468:20: note: in expansion of macro 'FREEMEMORY'
468 | if(cs->x[k].n) FREEMEMORY(NULL, cs->x[k].d);
| ^~~~~~~~~~
libs/bamio.c:468:5: note: some parts of macro expansion are not guarded by this 'if' clause
468 | if(cs->x[k].n) FREEMEMORY(NULL, cs->x[k].d);
| ^~
Building... library for source build/vqueue.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/vqueue.o libs/vqueue.c
Building... library for source build/aluruSort.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/aluruSort.o libs/aluruSort.c
Building... library for source build/segemehl_helper.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/segemehl_helper.o libs/segemehl_helper.c
Building... library for source build/bitArray.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/bitArray.o libs/bitArray.c
Building... library for source build/sw.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/sw.o libs/sw.c
Building... library for source build/kdchain.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/kdchain.o libs/kdchain.c
Building... library for source build/vtprogressbar.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/vtprogressbar.o libs/vtprogressbar.c
Building... library for source build/karlin.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/karlin.o libs/karlin.c
Building... library for source build/bgzip.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/bgzip.o libs/bgzip.c
Building... library for source build/gzidx.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/gzidx.o libs/gzidx.c
Building... library for source build/portable_endian.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/portable_endian.o libs/portable_endian.c
Building... library for source build/container.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/container.o libs/container.c
Building... library for source build/bedfiles.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/bedfiles.o libs/bedfiles.c
Building... library for source build/segemehl.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/segemehl.o libs/segemehl.c
Building... library for source build/memory.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/memory.o libs/memory.c
Building... library for source build/junctions.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/junctions.o libs/junctions.c
Building... library for source build/pigeon.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/pigeon.o libs/pigeon.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/radixsort.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/radixsort.o libs/radixsort.c
Building... library for source build/sort.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/sort.o libs/sort.c
Building... library for source build/match.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/match.o libs/match.c
Building... library for source build/charsequence.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -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)
| ^~
libs/charsequence.c: In function 'loadSequence':
libs/charsequence.c:296:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
296 | fread(s, sizeof(CharSequence), 1, infile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libs/charsequence.c:304:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
304 | fread(s->description, sizeof(char), s->descrlen+1, infile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libs/charsequence.c:305:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
305 | fread(s->alphabetname, sizeof(char), s->namelen+1, infile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libs/charsequence.c:306:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
306 | fread(s->url, sizeof(char), s->urllen+1, infile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libs/charsequence.c:307:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
307 | fread(sequence, sizeof(char), s->length, infile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Building... library for source build/stringutils.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/stringutils.o libs/stringutils.c
In file included from include/stringutils.h:27,
from libs/stringutils.c:39:
libs/stringutils.c: In function 'destructStringset':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/stringutils.c:274:9: note: in expansion of macro 'FREEMEMORY'
274 | FREEMEMORY(space, s->strings[i].str);
| ^~~~~~~~~~
libs/stringutils.c:273:7: note: some parts of macro expansion are not guarded by this 'if' clause
273 | if(s->strings[i].str != NULL)
| ^~
Building... library for source build/samio.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/samio.o libs/samio.c
Building... library for source build/manout.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/manout.o libs/manout.c
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from libs/samio.c:33:
libs/samio.c: In function 'bl_samDestructTag':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/samio.c:102:15: note: in expansion of macro 'FREEMEMORY'
102 | if(kv->tag) FREEMEMORY(NULL, kv->tag);
| ^~~~~~~~~~
libs/samio.c:102:3: note: some parts of macro expansion are not guarded by this 'if' clause
102 | if(kv->tag) FREEMEMORY(NULL, kv->tag);
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from libs/samio.c:33:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/samio.c:103:15: note: in expansion of macro 'FREEMEMORY'
103 | if(kv->val) FREEMEMORY(NULL, kv->val);
| ^~~~~~~~~~
libs/samio.c:103:3: note: some parts of macro expansion are not guarded by this 'if' clause
103 | if(kv->val) FREEMEMORY(NULL, kv->val);
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from libs/samio.c:33:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/samio.c:104:16: note: in expansion of macro 'FREEMEMORY'
104 | if(kv->type) FREEMEMORY(NULL, kv->type);
| ^~~~~~~~~~
libs/samio.c:104:3: note: some parts of macro expansion are not guarded by this 'if' clause
104 | if(kv->type) FREEMEMORY(NULL, kv->type);
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from libs/samio.c:33:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/samio.c:105:15: note: in expansion of macro 'FREEMEMORY'
105 | if(kv->key) FREEMEMORY(NULL, kv->key);
| ^~~~~~~~~~
libs/samio.c:105:3: note: some parts of macro expansion are not guarded by this 'if' clause
105 | if(kv->key) FREEMEMORY(NULL, kv->key);
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from libs/samio.c:33:
libs/samio.c: In function 'bl_samDestruct':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/samio.c:112:21: note: in expansion of macro 'FREEMEMORY'
112 | if(samrec->qname) FREEMEMORY(NULL, samrec->qname);
| ^~~~~~~~~~
libs/samio.c:112:3: note: some parts of macro expansion are not guarded by this 'if' clause
112 | if(samrec->qname) FREEMEMORY(NULL, samrec->qname);
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from libs/samio.c:33:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/samio.c:113:21: note: in expansion of macro 'FREEMEMORY'
113 | if(samrec->rname) FREEMEMORY(NULL, samrec->rname);
| ^~~~~~~~~~
libs/samio.c:113:3: note: some parts of macro expansion are not guarded by this 'if' clause
113 | if(samrec->rname) FREEMEMORY(NULL, samrec->rname);
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from libs/samio.c:33:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/samio.c:114:21: note: in expansion of macro 'FREEMEMORY'
114 | if(samrec->cigar) FREEMEMORY(NULL, samrec->cigar);
| ^~~~~~~~~~
libs/samio.c:114:3: note: some parts of macro expansion are not guarded by this 'if' clause
114 | if(samrec->cigar) FREEMEMORY(NULL, samrec->cigar);
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from libs/samio.c:33:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/samio.c:115:21: note: in expansion of macro 'FREEMEMORY'
115 | if(samrec->rnext) FREEMEMORY(NULL, samrec->rnext);
| ^~~~~~~~~~
libs/samio.c:115:3: note: some parts of macro expansion are not guarded by this 'if' clause
115 | if(samrec->rnext) FREEMEMORY(NULL, samrec->rnext);
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from libs/samio.c:33:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/samio.c:116:21: note: in expansion of macro 'FREEMEMORY'
116 | if(samrec->seq) FREEMEMORY(NULL, samrec->seq);
| ^~~~~~~~~~
libs/samio.c:116:3: note: some parts of macro expansion are not guarded by this 'if' clause
116 | if(samrec->seq) FREEMEMORY(NULL, samrec->seq);
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from libs/samio.c:33:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/samio.c:117:21: note: in expansion of macro 'FREEMEMORY'
117 | if(samrec->qual) FREEMEMORY(NULL, samrec->qual);
| ^~~~~~~~~~
libs/samio.c:117:3: note: some parts of macro expansion are not guarded by this 'if' clause
117 | if(samrec->qual) FREEMEMORY(NULL, samrec->qual);
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from libs/samio.c:33:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/samio.c:121:20: note: in expansion of macro 'FREEMEMORY'
121 | if(samrec->tags) FREEMEMORY(NULL, samrec->tags);
| ^~~~~~~~~~
libs/samio.c:121:3: note: some parts of macro expansion are not guarded by this 'if' clause
121 | if(samrec->tags) FREEMEMORY(NULL, samrec->tags);
| ^~
Building... library for source build/brendel.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/brendel.o libs/brendel.c
Building... library for source build/info.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/info.o libs/info.c
libs/info.c: In function 'timestr_r':
libs/info.c:64:50: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 12 [-Wformat-overflow=]
64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d",
| ^~
libs/info.c:64:21: note: directive argument in the range [-2147481748, 2147483647]
64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from libs/info.c:41:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 16 and 67 bytes into a destination of size 26
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from libs/info.c:41:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 16 and 67 bytes into a destination of size 26
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from libs/info.c:41:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 16 and 67 bytes into a destination of size 26
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Building... library for source build/gzip.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/gzip.o libs/gzip.c
libs/gzip.c: In function 'readCommonHeader':
libs/gzip.c:41:56: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
41 | fprintf(stderr, "common header has a length of %ld instead of %ld - not good.\n", bytesRead, sizeof(u_CommonHeader));
| ~~^ ~~~~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
libs/gzip.c:41:71: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'unsigned int' [-Wformat=]
41 | fprintf(stderr, "common header has a length of %ld instead of %ld - not good.\n", bytesRead, sizeof(u_CommonHeader));
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~
| | |
| long int unsigned int
| %d
Building... library for source build/sufarray.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/sufarray.o libs/sufarray.c
Building... library for source build/fileBins.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/fileBins.o libs/fileBins.c
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/sufarray.h:45,
from libs/sufarray.c:39:
libs/sufarray.c: In function 'destructSufArr':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/sufarray.c:613:5: note: in expansion of macro 'FREEMEMORY'
613 | FREEMEMORY(space, arr->lcpctab);
| ^~~~~~~~~~
libs/sufarray.c:612:3: note: some parts of macro expansion are not guarded by this 'if' clause
612 | if (arr->lcpctab != NULL)
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/sufarray.h:45,
from libs/sufarray.c:39:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/sufarray.c:615:5: note: in expansion of macro 'FREEMEMORY'
615 | FREEMEMORY(space, arr->inv_suftab);
| ^~~~~~~~~~
libs/sufarray.c:614:3: note: some parts of macro expansion are not guarded by this 'if' clause
614 | if (arr->inv_suftab != NULL)
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/sufarray.h:45,
from libs/sufarray.c:39:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/sufarray.c:619:5: note: in expansion of macro 'FREEMEMORY'
619 | FREEMEMORY(space, arr->idvtab);
| ^~~~~~~~~~
libs/sufarray.c:618:3: note: some parts of macro expansion are not guarded by this 'if' clause
618 | if (arr->idvtab != NULL)
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/sufarray.h:45,
from libs/sufarray.c:39:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/sufarray.c:624:5: note: in expansion of macro 'FREEMEMORY'
624 | FREEMEMORY(space, arr->suflink);
| ^~~~~~~~~~
libs/sufarray.c:620:3: note: some parts of macro expansion are not guarded by this 'if' clause
620 | if (arr->suflink != NULL)
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/sufarray.h:45,
from libs/sufarray.c:39:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/sufarray.c:627:5: note: in expansion of macro 'FREEMEMORY'
627 | FREEMEMORY(space, arr->chldtab);
| ^~~~~~~~~~
libs/sufarray.c:626:3: note: some parts of macro expansion are not guarded by this 'if' clause
626 | if (arr->chldtab != NULL)
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/sufarray.h:45,
from libs/sufarray.c:39:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/sufarray.c:629:5: note: in expansion of macro 'FREEMEMORY'
629 | FREEMEMORY(space, arr->mdfive);
| ^~~~~~~~~~
libs/sufarray.c:628:3: note: some parts of macro expansion are not guarded by this 'if' clause
628 | if (arr->mdfive)
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/sufarray.h:45,
from libs/sufarray.c:39:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/sufarray.c:631:5: note: in expansion of macro 'FREEMEMORY'
631 | FREEMEMORY(space, arr->llvtab);
| ^~~~~~~~~~
libs/sufarray.c:630:3: note: some parts of macro expansion are not guarded by this 'if' clause
630 | if(arr->llvtab != NULL)
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/sufarray.h:45,
from libs/sufarray.c:39:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/sufarray.c:636:5: note: in expansion of macro 'FREEMEMORY'
636 | FREEMEMORY(space, arr->id);
| ^~~~~~~~~~
libs/sufarray.c:632:3: note: some parts of macro expansion are not guarded by this 'if' clause
632 | if(arr->id != NULL)
| ^~
libs/sufarray.c: In function 'readSuffixarray':
libs/sufarray.c:428:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
428 | fread(&nmemb, sizeof(Uint), 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libs/sufarray.c:430:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
430 | fread(suftab, sizeof(Uint), nmemb, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libs/sufarray.c:431:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
431 | fread(&flags, sizeof(char), 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libs/sufarray.c:436:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
436 | fread(lcpctab, sizeof(unsigned char), nmemb, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libs/sufarray.c:438:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
438 | fread(&llvmemb, sizeof(Uint), 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libs/sufarray.c:440:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
440 | fread(llvtab, sizeof(PairUint), llvmemb, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libs/sufarray.c:446:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
446 | fread(chldtab, sizeof(childtab), nmemb, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libs/sufarray.c:484:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
484 | fread(suflink, sizeof(Uint), nmemb, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libs/sufarray.c:508:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
508 | fread(id, sizeof(signed char), nmemb, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libs/sufarray.c:511:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
511 | fread(&idvmemb, sizeof(Uint), 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libs/sufarray.c:515:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
515 | fread(idvtab, sizeof(PairLSint), idvmemb, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libs/sufarray.c:519:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
519 | fread(idvutab, sizeof(PairUint), idvmemb, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libs/sufarray.c:530:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
530 | fread(mdfive, sizeof(unsigned char), 16, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Building... library for source build/splitalign.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/splitalign.o libs/splitalign.c
In file included from libs/fileBins.c:51:
libs/fileBins.c: In function 'bl_fileBinsSortLine':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/fileBins.c:901:18: note: in expansion of macro 'FREEMEMORY'
901 | if(fileSort) FREEMEMORY(space, line);
| ^~~~~~~~~~
libs/fileBins.c:901:5: note: some parts of macro expansion are not guarded by this 'if' clause
901 | if(fileSort) FREEMEMORY(space, line);
| ^~
In file included from include/stringutils.h:27,
from include/biofiles.h:43,
from include/alignment.h:38,
from include/bitvectoralg.h:32,
from include/splitalign.h:29,
from libs/splitalign.c:32:
libs/splitalign.c: In function 'bl_fixSplitAlignHoffmann':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/splitalign.c:1323:25: note: in expansion of macro 'FREEMEMORY'
1323 | if(leftseedno[0]) FREEMEMORY(space, leftseeds[0]);
| ^~~~~~~~~~
libs/splitalign.c:1323:7: note: some parts of macro expansion are not guarded by this 'if' clause
1323 | if(leftseedno[0]) FREEMEMORY(space, leftseeds[0]);
| ^~
In file included from include/stringutils.h:27,
from include/biofiles.h:43,
from include/alignment.h:38,
from include/bitvectoralg.h:32,
from include/splitalign.h:29,
from libs/splitalign.c:32:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/splitalign.c:1324:25: note: in expansion of macro 'FREEMEMORY'
1324 | if(leftseedno[1]) FREEMEMORY(space, leftseeds[1]);
| ^~~~~~~~~~
libs/splitalign.c:1324:7: note: some parts of macro expansion are not guarded by this 'if' clause
1324 | if(leftseedno[1]) FREEMEMORY(space, leftseeds[1]);
| ^~
In file included from include/stringutils.h:27,
from include/biofiles.h:43,
from include/alignment.h:38,
from include/bitvectoralg.h:32,
from include/splitalign.h:29,
from libs/splitalign.c:32:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/splitalign.c:1325:26: note: in expansion of macro 'FREEMEMORY'
1325 | if(rightseedno[0]) FREEMEMORY(space, rightseeds[0]);
| ^~~~~~~~~~
libs/splitalign.c:1325:7: note: some parts of macro expansion are not guarded by this 'if' clause
1325 | if(rightseedno[0]) FREEMEMORY(space, rightseeds[0]);
| ^~
In file included from include/stringutils.h:27,
from include/biofiles.h:43,
from include/alignment.h:38,
from include/bitvectoralg.h:32,
from include/splitalign.h:29,
from libs/splitalign.c:32:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/splitalign.c:1326:26: note: in expansion of macro 'FREEMEMORY'
1326 | if(rightseedno[1]) FREEMEMORY(space, rightseeds[1]);
| ^~~~~~~~~~
libs/splitalign.c:1326:7: note: some parts of macro expansion are not guarded by this 'if' clause
1326 | if(rightseedno[1]) FREEMEMORY(space, rightseeds[1]);
| ^~
In file included from include/stringutils.h:27,
from include/biofiles.h:43,
from include/alignment.h:38,
from include/bitvectoralg.h:32,
from include/splitalign.h:29,
from libs/splitalign.c:32:
libs/splitalign.c: In function 'bl_fixSplitAlignBrendel':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/splitalign.c:1565:27: note: in expansion of macro 'FREEMEMORY'
1565 | if(leftseedno[0]) FREEMEMORY(space, leftseeds[0]);
| ^~~~~~~~~~
libs/splitalign.c:1565:9: note: some parts of macro expansion are not guarded by this 'if' clause
1565 | if(leftseedno[0]) FREEMEMORY(space, leftseeds[0]);
| ^~
In file included from include/stringutils.h:27,
from include/biofiles.h:43,
from include/alignment.h:38,
from include/bitvectoralg.h:32,
from include/splitalign.h:29,
from libs/splitalign.c:32:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/splitalign.c:1566:27: note: in expansion of macro 'FREEMEMORY'
1566 | if(leftseedno[1]) FREEMEMORY(space, leftseeds[1]);
| ^~~~~~~~~~
libs/splitalign.c:1566:9: note: some parts of macro expansion are not guarded by this 'if' clause
1566 | if(leftseedno[1]) FREEMEMORY(space, leftseeds[1]);
| ^~
In file included from include/stringutils.h:27,
from include/biofiles.h:43,
from include/alignment.h:38,
from include/bitvectoralg.h:32,
from include/splitalign.h:29,
from libs/splitalign.c:32:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/splitalign.c:1567:28: note: in expansion of macro 'FREEMEMORY'
1567 | if(rightseedno[0]) FREEMEMORY(space, rightseeds[0]);
| ^~~~~~~~~~
libs/splitalign.c:1567:9: note: some parts of macro expansion are not guarded by this 'if' clause
1567 | if(rightseedno[0]) FREEMEMORY(space, rightseeds[0]);
| ^~
In file included from include/stringutils.h:27,
from include/biofiles.h:43,
from include/alignment.h:38,
from include/bitvectoralg.h:32,
from include/splitalign.h:29,
from libs/splitalign.c:32:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/splitalign.c:1568:28: note: in expansion of macro 'FREEMEMORY'
1568 | if(rightseedno[1]) FREEMEMORY(space, rightseeds[1]);
| ^~~~~~~~~~
libs/splitalign.c:1568:9: note: some parts of macro expansion are not guarded by this 'if' clause
1568 | if(rightseedno[1]) FREEMEMORY(space, rightseeds[1]);
| ^~
Building... library for source build/iupac.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/iupac.o libs/iupac.c
Building... library for source build/bitvectoralg.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/bitvectoralg.o libs/bitvectoralg.c
Building... library for source build/intervaltree.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/intervaltree.o libs/intervaltree.c
In file included from include/mathematics.h:117,
from libs/intervaltree.c:27:
libs/intervaltree.c: In function 'bl_intervaltreeDestruct':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/intervaltree.c:443:19: note: in expansion of macro 'FREEMEMORY'
443 | if(root->ncoll) FREEMEMORY(NULL, root->collisions);
| ^~~~~~~~~~
libs/intervaltree.c:443:3: note: some parts of macro expansion are not guarded by this 'if' clause
443 | if(root->ncoll) FREEMEMORY(NULL, root->collisions);
| ^~
Building... library for source build/haarz.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/haarz.o libs/haarz.c
Building... library for source build/manopt.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/manopt.o libs/manopt.c
Building... library for source build/mathematics.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/mathematics.o libs/mathematics.c
In file included from include/mathematics.h:117,
from libs/mathematics.c:38:
libs/mathematics.c: In function 'destructVector':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/mathematics.c:251:23: note: in expansion of macro 'FREEMEMORY'
251 | if (v->elements) FREEMEMORY(space, v->elements);
| ^~~~~~~~~~
libs/mathematics.c:251:6: note: some parts of macro expansion are not guarded by this 'if' clause
251 | if (v->elements) FREEMEMORY(space, v->elements);
| ^~
Building... library for source build/multicharseq.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/multicharseq.o libs/multicharseq.c
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from libs/multicharseq.c:38:
libs/multicharseq.c: In function 'destructMultiCharSeq':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/multicharseq.c:212:7: note: in expansion of macro 'FREEMEMORY'
212 | FREEMEMORY(space, mseq->markpos);
| ^~~~~~~~~~
libs/multicharseq.c:211:2: note: some parts of macro expansion are not guarded by this 'if' clause
211 | if (mseq->markpos != NULL)
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from libs/multicharseq.c:38:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/multicharseq.c:214:7: note: in expansion of macro 'FREEMEMORY'
214 | FREEMEMORY(space, mseq->map);
| ^~~~~~~~~~
libs/multicharseq.c:213:2: note: some parts of macro expansion are not guarded by this 'if' clause
213 | if (mseq->map != NULL)
| ^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from libs/multicharseq.c:38:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
| ^~~~
libs/multicharseq.c:216:7: note: in expansion of macro 'FREEMEMORY'
216 | FREEMEMORY(space, mseq->ref);
| ^~~~~~~~~~
libs/multicharseq.c:215:5: note: some parts of macro expansion are not guarded by this 'if' clause
215 | if (mseq->ref != NULL)
| ^~
Building... library for source build/filebuffer.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/filebuffer.o libs/filebuffer.c
Building... library for source build/mapfrag.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/mapfrag.o libs/mapfrag.c
Building... library for source build/mappingqual.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/mappingqual.o libs/mappingqual.c
Building... library for source build/nw.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/nw.o libs/nw.c
Building... library for source build/alignment.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -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]);
| ^~
Building... library for source build/biofiles.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/biofiles.o libs/biofiles.c
Building... library for source build/fileio.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/fileio.o libs/fileio.c
libs/fileio.c: In function 'bl_rm':
libs/fileio.c:220:3: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
220 | system(cmd);
| ^~~~~~~~~~~
Building... library for source build/merge.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -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/samheader.o
cc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/samheader.o libs/samheader.c
Linking segemehl
Linking haarz
cc build/md5.o build/vstack.o build/queryalign.o build/annotation.o build/bitVector.o build/locus.o build/seqclip.o build/debug.o build/kdseed.o build/stack.o build/bamio.o build/vqueue.o build/aluruSort.o build/segemehl_helper.o build/bitArray.o build/sw.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/biofiles.o build/fileio.o build/merge.o build/samheader.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
cc build/md5.o build/vstack.o build/queryalign.o build/annotation.o build/bitVector.o build/locus.o build/seqclip.o build/debug.o build/kdseed.o build/stack.o build/bamio.o build/vqueue.o build/aluruSort.o build/segemehl_helper.o build/bitArray.o build/sw.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/biofiles.o build/fileio.o build/merge.o build/samheader.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
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
create-stamp debian/debhelper-build-stamp
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_installexamples -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_dwz -a -a
dh_strip -a -a
dh_makeshlibs -a -a
dh_shlibdeps -a -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_0.3.4-5_armhf.deb'.
dpkg-deb: building package 'segemehl-dbgsym' in '../segemehl-dbgsym_0.3.4-5_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../segemehl_0.3.4-5_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2021-08-27T11:29:10Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
segemehl_0.3.4-5_armhf.changes:
-------------------------------
Format: 1.8
Date: Tue, 24 Aug 2021 22:19:01 +0530
Source: segemehl
Binary: segemehl segemehl-dbgsym
Architecture: armhf
Version: 0.3.4-5
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Nilesh Patra <nilesh@debian.org>
Description:
segemehl - short read mapping with gaps
Changes:
segemehl (0.3.4-5) unstable; urgency=medium
.
* Team Upload.
* d/p/arm64.patch: Fix segfaults on !amd64 and !i386
* Bump Standards-Version to 4.6.0 (no changes needed)
Checksums-Sha1:
922d610ac1cc7abccc1c199bb63486d87a408033 1492944 segemehl-dbgsym_0.3.4-5_armhf.deb
91ca60cc402b313488a8f0cc5db49345d5f70c62 5658 segemehl_0.3.4-5_armhf.buildinfo
4a630fb887f7c3e1c372793d8b5bb14457d4df04 222980 segemehl_0.3.4-5_armhf.deb
Checksums-Sha256:
6a651223c0dff3165e2b46d9b34fff322795232b33b27f510507a3aebc9eb2fe 1492944 segemehl-dbgsym_0.3.4-5_armhf.deb
0b2bbad1665c32f0ec05783bfcca73a6edfded8dce0c28ce60f43000647000c9 5658 segemehl_0.3.4-5_armhf.buildinfo
b3cd5c6c4d50f014383527fa12900bdd293b5eeb23d367b3bc5c45346e64e1a4 222980 segemehl_0.3.4-5_armhf.deb
Files:
ce71b85ad3bafe0fb2d640a2f142be65 1492944 debug optional segemehl-dbgsym_0.3.4-5_armhf.deb
929d77476cc531cd2e93614f8e71e47a 5658 science optional segemehl_0.3.4-5_armhf.buildinfo
5264d1e7168e324a1b66449b6295549e 222980 science optional segemehl_0.3.4-5_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
segemehl-dbgsym_0.3.4-5_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 1492944 bytes: control archive=644 bytes.
416 bytes, 12 lines control
300 bytes, 3 lines md5sums
Package: segemehl-dbgsym
Source: segemehl
Version: 0.3.4-5
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1615
Depends: segemehl (= 0.3.4-5)
Section: debug
Priority: optional
Description: debug symbols for segemehl
Build-Ids: 0be5a894ed434a288e5b75c4643e09210111711e 534821b9665bebc6ab332f1e3ea2364469b75aea
drwxr-xr-x root/root 0 2021-08-24 16:49 ./
drwxr-xr-x root/root 0 2021-08-24 16:49 ./usr/
drwxr-xr-x root/root 0 2021-08-24 16:49 ./usr/lib/
drwxr-xr-x root/root 0 2021-08-24 16:49 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-08-24 16:49 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-08-24 16:49 ./usr/lib/debug/.build-id/0b/
-rw-r--r-- root/root 798148 2021-08-24 16:49 ./usr/lib/debug/.build-id/0b/e5a894ed434a288e5b75c4643e09210111711e.debug
drwxr-xr-x root/root 0 2021-08-24 16:49 ./usr/lib/debug/.build-id/53/
-rw-r--r-- root/root 799112 2021-08-24 16:49 ./usr/lib/debug/.build-id/53/4821b9665bebc6ab332f1e3ea2364469b75aea.debug
drwxr-xr-x root/root 0 2021-08-24 16:49 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2021-08-24 16:49 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 41920 2021-08-24 16:49 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/segemehl.debug
drwxr-xr-x root/root 0 2021-08-24 16:49 ./usr/share/
drwxr-xr-x root/root 0 2021-08-24 16:49 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-08-24 16:49 ./usr/share/doc/segemehl-dbgsym -> segemehl
segemehl_0.3.4-5_armhf.deb
--------------------------
new Debian package, version 2.0.
size 222980 bytes: control archive=1484 bytes.
1607 bytes, 29 lines control
737 bytes, 11 lines md5sums
Package: segemehl
Version: 0.3.4-5
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1000
Depends: libc6 (>= 2.29), libhts3 (>= 1.10), zlib1g (>= 1:1.2.2.4)
Section: science
Priority: optional
Homepage: http://www.bioinf.uni-leipzig.de/Software/segemehl/
Description: short read mapping with gaps
Segemehl is a software to map short sequencer reads to reference
genomes. Segemehl implements a matching strategy based on enhanced
suffix arrays (ESA). Segemehl accepts fasta and fastq queries (gzip'ed
and bgzip'ed). In addition to the alignment of reads from standard DNA-
and RNA-seq protocols, it also allows the mapping of bisulfite converted
reads (Lister and Cokus) and implements a split read mapping strategy.
The output of segemehl is a SAM or BAM formatted alignment file. In the
case of split-read mapping, additional BED files are written to the
disc. These BED files may be summarized with the postprocessing tool
haarz. In the case of the alignment of bisulfite converted reads, raw
methylation rates may also be called with haarz.
.
In brief, for each suffix of a read, segemehl aims to find the
best-scoring seed. Seeds might contain insertions, deletions, and
mismatches (differences). The number of differences allowed within a
single seed is user-controlled and is crucial for the runtime of the
program. Subsequently, seeds that undercut the user-defined E-value are
passed on to an exact semi-global alignment procedure. Finally, reads
with a minimum accuracy of percent are reported to the user.
drwxr-xr-x root/root 0 2021-08-24 16:49 ./
drwxr-xr-x root/root 0 2021-08-24 16:49 ./usr/
drwxr-xr-x root/root 0 2021-08-24 16:49 ./usr/bin/
-rwxr-xr-x root/root 497908 2021-08-24 16:49 ./usr/bin/haarz
-rwxr-xr-x root/root 502072 2021-08-24 16:49 ./usr/bin/segemehl
drwxr-xr-x root/root 0 2021-08-24 16:49 ./usr/share/
drwxr-xr-x root/root 0 2021-08-24 16:49 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-08-24 16:49 ./usr/share/doc/segemehl/
-rw-r--r-- root/root 545 2021-08-01 11:38 ./usr/share/doc/segemehl/README.test
-rw-r--r-- root/root 710 2021-08-24 16:49 ./usr/share/doc/segemehl/changelog.Debian.gz
-rw-r--r-- root/root 1108 2021-08-16 11:22 ./usr/share/doc/segemehl/copyright
drwxr-xr-x root/root 0 2021-08-24 16:49 ./usr/share/doc/segemehl/examples/
-rw-r--r-- root/root 75 2021-08-01 11:38 ./usr/share/doc/segemehl/examples/myseq.fa
-rw-r--r-- root/root 258 2021-08-01 11:38 ./usr/share/doc/segemehl/examples/seq1.fa
-rw-r--r-- root/root 93 2021-08-01 11:38 ./usr/share/doc/segemehl/examples/seq2.fa
-rw-r--r-- root/root 548 2021-08-24 16:48 ./usr/share/doc/segemehl/run-unit-test
drwxr-xr-x root/root 0 2021-08-24 16:49 ./usr/share/man/
drwxr-xr-x root/root 0 2021-08-24 16:49 ./usr/share/man/man1/
-rw-r--r-- root/root 505 2021-08-24 16:49 ./usr/share/man/man1/haarz.1.gz
-rw-r--r-- root/root 2427 2021-08-24 16:49 ./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: 15616
Build-Time: 116
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 275
Job: segemehl_0.3.4-5
Machine Architecture: armhf
Package: segemehl
Package-Time: 443
Source-Version: 0.3.4-5
Space: 15616
Status: successful
Version: 0.3.4-5
--------------------------------------------------------------------------------
Finished at 2021-08-27T11:29:10Z
Build needed 00:07:23, 15616k disc space