segemehl →
0.3.4-1 →
armhf → 2019-01-17 06:38:53
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-04
+==============================================================================+
| segemehl 0.3.4-1 (armhf) Thu, 17 Jan 2019 06:29:51 +0000 |
+==============================================================================+
Package: segemehl
Version: 0.3.4-1
Source Version: 0.3.4-1
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-085584d0-75d1-402e-8a71-b680e1026eee' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [11.4 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [13.2 MB]
Fetched 24.6 MB in 28s (866 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'segemehl' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/segemehl.git
Please use:
git clone https://salsa.debian.org/med-team/segemehl.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 252 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main segemehl 0.3.4-1 (dsc) [2000 B]
Get:2 http://172.17.0.1/private buster-staging/main segemehl 0.3.4-1 (tar) [244 kB]
Get:3 http://172.17.0.1/private buster-staging/main segemehl 0.3.4-1 (diff) [5536 B]
Fetched 252 kB in 0s (4042 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/segemehl-R7Cai9/segemehl-0.3.4' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/segemehl-R7Cai9' 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-5mnMhF/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-5mnMhF/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-5mnMhF/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-5mnMhF/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-5mnMhF/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-5mnMhF/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-5mnMhF/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-5mnMhF/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (3033 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session krb5-locales libexpat1
libgpg-error-l10n libnss-systemd libpam-systemd libssl1.1 openssl
systemd-sysv
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 26 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-5mnMhF/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 14046 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 (>= 12~), pkg-config, libhts-dev, libncurses-dev, zlib1g-dev
Filtered Build-Depends: debhelper (>= 12~), pkg-config, libhts-dev, libncurses-dev, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-segemehl-dummy' in '/<<BUILDDIR>>/resolver-5mnMhF/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-5mnMhF/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-5mnMhF/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-5mnMhF/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-5mnMhF/apt_archive ./ Sources [520 B]
Get:5 copy:/<<BUILDDIR>>/resolver-5mnMhF/apt_archive ./ Packages [602 B]
Fetched 2455 B in 1s (3435 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 packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session krb5-locales libexpat1
libgpg-error-l10n libnss-systemd libpam-systemd openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3
libcurl3-gnutls libelf1 libfile-stripnondeterminism-perl libglib2.0-0
libhts-dev libhts2 libicu63 liblzma-dev libmagic-mgc libmagic1
libncurses-dev libnghttp2-14 libpipeline1 libpsl5 librtmp1 libsigsegv2
libssh2-1 libtool libuchardet0 libxml2 m4 man-db pkg-config po-debconf
zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
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 libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs publicsuffix libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3
libcurl3-gnutls libelf1 libfile-stripnondeterminism-perl libglib2.0-0
libhts-dev libhts2 libicu63 liblzma-dev libmagic-mgc libmagic1
libncurses-dev libnghttp2-14 libpipeline1 libpsl5 librtmp1 libsigsegv2
libssh2-1 libtool libuchardet0 libxml2 m4 man-db pkg-config po-debconf
sbuild-build-depends-segemehl-dummy zlib1g-dev
0 upgraded, 43 newly installed, 0 to remove and 26 not upgraded.
Need to get 23.5 MB/23.9 MB of archives.
After this operation, 75.7 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-5mnMhF/apt_archive ./ sbuild-build-depends-segemehl-dummy 0.invalid.0 [884 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.4-2 [782 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-2 [25.1 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.5-1 [1231 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.34-2 [239 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.34-2 [107 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.34-2 [65.0 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-2 [185 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-6 [547 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 1.1.0-1 [19.5 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 1.1.0-1 [12.6 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.175-2 [157 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-3 [66.0 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.58.2-3 [1076 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libicu63 armhf 63.1-5 [7976 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+b1 [570 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-3 [132 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf debhelper all 12 [1002 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.35.1-1 [70.8 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.0 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-2 [125 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.62.0-1 [284 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libhts2 armhf 1.9-8 [254 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libhts-dev armhf 1.9-8 [4280 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libncurses-dev armhf 6.1+20181013-1 [278 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Processing triggers for libc-bin (2.28-2) ...
Setting up dwz (0.12-3) ...
Setting up autotools-dev (20180224.1) ...
Setting up liblzma-dev:armhf (5.2.2-1.3) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libncurses-dev:armhf (6.1+20181013-1) ...
Setting up autopoint (0.19.8.1-9) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up libfile-stripnondeterminism-perl (1.1.0-1) ...
Setting up gettext (0.19.8.1-9) ...
Setting up libcurl3-gnutls:armhf (7.62.0-1) ...
Setting up groff-base (1.22.4-2) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.34-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.8.5-1) ...
Not building database; man-db/auto-update is not 'true'.
Created symlink /etc/systemd/system/timers.target.wants/man-db.timer -> /lib/systemd/system/man-db.timer.
Setting up libhts2:armhf (1.9-8) ...
Setting up libtool (2.4.6-6) ...
Setting up po-debconf (1.0.21) ...
Setting up libhts-dev:armhf (1.9-8) ...
Setting up dh-autoreconf (19) ...
Setting up dh-strip-nondeterminism (1.1.0-1) ...
Setting up debhelper (12) ...
Setting up sbuild-build-depends-segemehl-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.28-2) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.4-armmp armhf (armv7l)
Toolchain package versions: binutils_2.31.1-11+rpi1 dpkg-dev_1.19.2 g++-8_8.2.0-13+rpi1 gcc-8_8.2.0-13+rpi1 libc6-dev_2.28-2 libstdc++-8-dev_8.2.0-13+rpi1 libstdc++6_8.2.0-13+rpi1 linux-libc-dev_4.18.20-2+rpi1
Package versions: adduser_3.118 apt_1.8.0~alpha3 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-3.1 binutils_2.31.1-11+rpi1 binutils-arm-linux-gnueabihf_2.31.1-11+rpi1 binutils-common_2.31.1-11+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.33.1-0.1 build-essential_12.5 bzip2_1.0.6-9 ca-certificates_20170717 coreutils_8.30-1 cpio_2.12+dfsg-6 cpp_4:8.2.0-2+rpi1 cpp-8_8.2.0-13+rpi1 dash_0.5.10.2-4 dbus_1.12.12-1 dbus-user-session_1.12.12-1 debconf_1.5.69 debhelper_12 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_1.1.0-1 diffutils_1:3.6-1 dirmngr_2.2.12-1+rpi1 dmsetup_2:1.02.155-1 dpkg_1.19.2 dpkg-dev_1.19.2 dwz_0.12-3 e2fslibs_1.44.5-1 e2fsprogs_1.44.5-1 fakeroot_1.23-1 fdisk_2.33.1-0.1 file_1:5.34-2 findutils_4.6.0+git+20181018-1 g++_4:8.2.0-2+rpi1 g++-8_8.2.0-13+rpi1 gcc_4:8.2.0-2+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-6-base_6.5.0-1+rpi1 gcc-8_8.2.0-13+rpi1 gcc-8-base_8.2.0-13+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gnupg_2.2.12-1+rpi1 gnupg-l10n_2.2.12-1+rpi1 gnupg-utils_2.2.12-1+rpi1 gpg_2.2.12-1+rpi1 gpg-agent_2.2.12-1+rpi1 gpg-wks-client_2.2.12-1+rpi1 gpg-wks-server_2.2.12-1+rpi1 gpgconf_2.2.12-1+rpi1 gpgsm_2.2.12-1+rpi1 gpgv_2.2.12-1+rpi1 grep_3.1-3 groff-base_1.22.4-2 gzip_1.9-3 hostname_3.21 inetutils-ping_2:1.9.4-5 init-system-helpers_1.56+nmu1 initramfs-tools_0.132 initramfs-tools-core_0.132 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-14+rpi1 kmod_25-2 krb5-locales_1.16.2-1 libacl1_2.2.52-3 libapparmor1_2.13.2-3 libapt-pkg5.0_1.8.0~alpha3 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.1 libasan5_8.2.0-13+rpi1 libassuan0_2.5.2-1 libatomic1_8.2.0-13+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2+b1 libbinutils_2.31.1-11+rpi1 libblkid1_2.33.1-0.1 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.28-2 libc-dev-bin_2.28-2 libc6_2.28-2 libc6-dev_2.28-2 libcap-ng0_0.7.9-1+b1 libcap2_1:2.25-1.2 libcc1-0_8.2.0-13+rpi1 libcom-err2_1.44.5-1 libcroco3_0.6.12-3 libcryptsetup12_2:2.0.6-1 libcryptsetup4_2:1.7.5-1 libcurl3-gnutls_7.62.0-1 libdb5.3_5.3.28+dfsg1-0.2 libdbus-1-3_1.12.12-1 libdebconfclient0_0.246 libdevmapper1.02.1_2:1.02.155-1 libdpkg-perl_1.19.2 libdrm-common_2.4.95-1+rpi1 libdrm2_2.4.95-1+rpi1 libelf1_0.175-2 libexpat1_2.2.6-1 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.1.0-1 libgcc-8-dev_8.2.0-13+rpi1 libgcc1_1:8.2.0-13+rpi1 libgcrypt20_1.8.4-4 libgdbm-compat4_1.18.1-2 libgdbm3_1.8.3-14 libgdbm6_1.18.1-2 libglib2.0-0_2.58.2-3 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.5-2+rpi1 libgomp1_8.2.0-13+rpi1 libgpg-error-l10n_1.33-3 libgpg-error0_1.33-3 libgssapi-krb5-2_1.16.2-1 libhogweed4_3.4.1~rc1-1 libhts-dev_1.9-8 libhts2_1.9-8 libicu63_63.1-5 libidn11_1.33-2.2 libidn2-0_2.0.5-1 libip4tc0_1.8.2-3 libisl19_0.20-2 libjson-c3_0.12.1-1.3 libk5crypto3_1.16.2-1 libkeyutils1_1.5.9-9.3 libklibc_2.0.4-14+rpi1 libkmod2_25-2 libkrb5-3_1.16.2-1 libkrb5support0_1.16.2-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.47+dfsg-1 libldap-common_2.4.47+dfsg-1 liblz4-1_1.8.3-1 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.33.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.1-2 libncurses-dev_6.1+20181013-1 libncurses5_6.1+20181013-1 libncurses6_6.1+20181013-1 libncursesw5_6.1+20181013-1 libncursesw6_6.1+20181013-1 libnettle6_3.4.1~rc1-1 libnghttp2-14_1.35.1-1 libnpth0_1.6-1 libnss-systemd_240-2+rpi1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-3.8 libpam-modules-bin_1.1.8-3.8 libpam-runtime_1.1.8-3.8 libpam-systemd_240-2+rpi1 libpam0g_1.1.8-3.8 libpcre3_2:8.39-11+rpi1 libperl5.28_5.28.1-3 libpipeline1_1.5.0-2 libplymouth4_0.9.4-1 libpng16-16_1.6.36-2 libprocps7_2:3.3.15-2 libpsl5_0.20.2-2 libreadline7_7.0-5 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27~rc8-1 libsasl2-modules-db_2.1.27~rc8-1 libseccomp2_2.3.3-3+b1 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33.1-0.1 libsqlite3-0_3.26.0+fossilbc891ac6b-1 libss2_1.44.5-1 libssh2-1_1.8.0-2 libssl1.1_1.1.1a-1 libstdc++-8-dev_8.2.0-13+rpi1 libstdc++6_8.2.0-13+rpi1 libsystemd0_240-2+rpi1 libtasn1-6_4.13-3 libtinfo5_6.1+20181013-1 libtinfo6_6.1+20181013-1 libtool_2.4.6-6 libubsan1_8.2.0-13+rpi1 libuchardet0_0.0.6-3 libudev1_240-2+rpi1 libunistring2_0.9.10-1 libuuid1_2.33.1-0.1 libxml2_2.9.4+dfsg1-7+b1 libzstd1_1.3.8+dfsg-3+rpi1 linux-base_4.5 linux-libc-dev_4.18.20-2+rpi1 login_1:4.5-1.1 lsb-base_10.2018112800+rpi1 m4_1.4.18-2 make_4.2.1-1.2 makedev_2.3.1-94 man-db_2.8.5-1 mawk_1.3.3-17 mount_2.33.1-0.1 multiarch-support_2.28-2 nano_3.2-1 ncurses-base_6.1+20181013-1 ncurses-bin_6.1+20181013-1 netbase_5.5 openssl_1.1.1a-1 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-3 perl-base_5.28.1-3 perl-modules-5.28_5.28.1-3 pinentry-curses_1.1.0-1 pkg-config_0.29-4 plymouth_0.9.4-1 po-debconf_1.0.21 procps_2:3.3.15-2 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-segemehl-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 systemd_240-2+rpi1 systemd-sysv_240-2+rpi1 sysvinit-utils_2.93-3 tar_1.30+dfsg-4 tzdata_2018i-1 udev_240-2+rpi1 util-linux_2.33.1-0.1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Fri Jan 11 21:54:08 2019 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./segemehl_0.3.4-1.dsc
dpkg-source: info: extracting segemehl in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking segemehl_0.3.4.orig.tar.xz
dpkg-source: info: unpacking segemehl_0.3.4-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying rpath.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=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-085584d0-75d1-402e-8a71-b680e1026eee
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package segemehl
dpkg-buildpackage: info: source version 0.3.4-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_auto_clean
make -j4 clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Cleaning...
rm -f -r build segemehl haarz
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build -- all
make -j4 "INSTALL=install --strip-program=true" all
make[2]: Entering directory '/<<PKGBUILDDIR>>'
Building... library for source build/md5.o
Building... library for source build/vstack.o
Building... library for source build/queryalign.o
Building... library for source build/annotation.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/md5.o libs/md5.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/queryalign.o libs/queryalign.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/vstack.o libs/vstack.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/annotation.o libs/annotation.c
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/annotation.c:149:23: note: in expansion of macro 'FREEMEMORY'
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
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/annotation.c:150:18: note: in expansion of macro 'FREEMEMORY'
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
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/annotation.c:151:21: note: in expansion of macro 'FREEMEMORY'
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
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/annotation.c:152:24: note: in expansion of macro 'FREEMEMORY'
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
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/annotation.c:153:25: note: in expansion of macro 'FREEMEMORY'
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
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/annotation.c:154:26: note: in expansion of macro 'FREEMEMORY'
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
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/annotation.c:155:26: note: in expansion of macro 'FREEMEMORY'
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
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/annotation.c:156:20: note: in expansion of macro 'FREEMEMORY'
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
if(item->source) FREEMEMORY(space, item->source);
^~
Building... library for source build/biofiles.o
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/annotation.c:409:24: note: in expansion of macro 'FREEMEMORY'
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
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/annotation.c:410:23: note: in expansion of macro 'FREEMEMORY'
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
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/annotation.c:411:26: note: in expansion of macro 'FREEMEMORY'
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
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/annotation.c:418:20: note: in expansion of macro 'FREEMEMORY'
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
if(track->items) FREEMEMORY(space, track->items) ;
^~
In file included from include/stringutils.h:27,
from libs/annotation.c:29:
libs/annotation.c: In function 'bl_annotationmultitrackDestruct':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/annotation.c:455:20: note: in expansion of macro 'FREEMEMORY'
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
if(track->items) FREEMEMORY(space, track->items) ;
^~
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/biofiles.o libs/biofiles.c
Building... library for source build/bitVector.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/bitVector.o libs/bitVector.c
Building... library for source build/locus.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/locus.o libs/locus.c
Building... library for source build/seqclip.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/seqclip.o libs/seqclip.c
In file included from include/stringutils.h:27,
from include/biofiles.h:43,
from include/alignment.h:38,
from include/sw.h:38,
from libs/seqclip.c:44:
libs/seqclip.c: In function 'bl_Find3PrimeGreedy':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/seqclip.c:529:9: note: in expansion of macro 'FREEMEMORY'
FREEMEMORY(space, adapter);
^~~~~~~~~~
libs/seqclip.c:528:7: note: some parts of macro expansion are not guarded by this 'if' clause
if(adapter)
^~
Building... library for source build/debug.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/debug.o libs/debug.c
Building... library for source build/merge.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/merge.o libs/merge.c
In file included from include/stringutils.h:27,
from libs/merge.c:34:
libs/merge.c: In function 'se_mergeWorker':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/merge.c:1096:20: note: in expansion of macro 'FREEMEMORY'
if(curkey) FREEMEMORY(NULL, curkey);
^~~~~~~~~~
libs/merge.c:1096:9: note: some parts of macro expansion are not guarded by this 'if' clause
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/merge.c:1216:26: note: in expansion of macro 'FREEMEMORY'
if(!reads && curkey) FREEMEMORY(NULL, curkey);
^~~~~~~~~~
libs/merge.c:1216:5: note: some parts of macro expansion are not guarded by this 'if' clause
if(!reads && curkey) FREEMEMORY(NULL, curkey);
^~
Building... library for source build/kdseed.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/kdseed.o libs/kdseed.c
Building... library for source build/stack.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/stack.o libs/stack.c
Building... library for source build/bamio.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/bamio.o libs/bamio.c
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from include/bamio.h:21,
from libs/bamio.c:32:
libs/bamio.c: In function 'bl_bamCrossSectionDestruct':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/bamio.c:468:20: note: in expansion of macro 'FREEMEMORY'
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
if(cs->x[k].n) FREEMEMORY(NULL, cs->x[k].d);
^~
Building... library for source build/vqueue.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/vqueue.o libs/vqueue.c
Building... library for source build/aluruSort.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/aluruSort.o libs/aluruSort.c
Building... library for source build/segemehl_helper.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/segemehl_helper.o libs/segemehl_helper.c
Building... library for source build/bitArray.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/bitArray.o libs/bitArray.c
Building... library for source build/samheader.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/samheader.o libs/samheader.c
Building... library for source build/sw.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/sw.o libs/sw.c
Building... library for source build/fileio.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/fileio.o libs/fileio.c
Building... library for source build/kdchain.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/kdchain.o libs/kdchain.c
Building... library for source build/vtprogressbar.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/vtprogressbar.o libs/vtprogressbar.c
Building... library for source build/karlin.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/karlin.o libs/karlin.c
Building... library for source build/bgzip.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/bgzip.o libs/bgzip.c
Building... library for source build/gzidx.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/gzidx.o libs/gzidx.c
Building... library for source build/portable_endian.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/portable_endian.o libs/portable_endian.c
Building... library for source build/container.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/container.o libs/container.c
Building... library for source build/bedfiles.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/bedfiles.o libs/bedfiles.c
Building... library for source build/segemehl.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/segemehl.o libs/segemehl.c
Building... library for source build/memory.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/memory.o libs/memory.c
Building... library for source build/junctions.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/junctions.o libs/junctions.c
Building... library for source build/pigeon.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/pigeon.o libs/pigeon.c
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/pigeon.c:352:13: note: in expansion of macro 'FREEMEMORY'
if(check) FREEMEMORY(space, check);
^~~~~~~~~~
libs/pigeon.c:352:3: note: some parts of macro expansion are not guarded by this 'if' clause
if(check) FREEMEMORY(space, check);
^~
Building... library for source build/radixsort.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/radixsort.o libs/radixsort.c
Building... library for source build/sort.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/sort.o libs/sort.c
Building... library for source build/match.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/match.o libs/match.c
Building... library for source build/charsequence.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/charsequence.o libs/charsequence.c
In file included from libs/charsequence.c:26:
libs/charsequence.c: In function 'destructSequence':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/charsequence.c:467:4: note: in expansion of macro 'FREEMEMORY'
FREEMEMORY(space, sequence->sequence);
^~~~~~~~~~
libs/charsequence.c:466:3: note: some parts of macro expansion are not guarded by this 'if' clause
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/charsequence.c:470:5: note: in expansion of macro 'FREEMEMORY'
FREEMEMORY(space, sequence->alphabetname);
^~~~~~~~~~
libs/charsequence.c:469:2: note: some parts of macro expansion are not guarded by this 'if' clause
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/charsequence.c:472:2: note: in expansion of macro 'FREEMEMORY'
FREEMEMORY(space, sequence->url);
^~~~~~~~~~
libs/charsequence.c:471:5: note: some parts of macro expansion are not guarded by this 'if' clause
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/charsequence.c:474:2: note: in expansion of macro 'FREEMEMORY'
FREEMEMORY(space, sequence->info);
^~~~~~~~~~
libs/charsequence.c:473:5: note: some parts of macro expansion are not guarded by this 'if' clause
if (sequence->info != NULL)
^~
Building... library for source build/stringutils.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/stringutils.o libs/stringutils.c
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/stringutils.c:274:9: note: in expansion of macro 'FREEMEMORY'
FREEMEMORY(space, s->strings[i].str);
^~~~~~~~~~
libs/stringutils.c:273:7: note: some parts of macro expansion are not guarded by this 'if' clause
if(s->strings[i].str != NULL)
^~
Building... library for source build/samio.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/samio.o libs/samio.c
Building... library for source build/manout.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/manout.o libs/manout.c
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from libs/samio.c:33:
libs/samio.c: In function 'bl_samDestructTag':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/samio.c:102:15: note: in expansion of macro 'FREEMEMORY'
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
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/samio.c:103:15: note: in expansion of macro 'FREEMEMORY'
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
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/samio.c:104:16: note: in expansion of macro 'FREEMEMORY'
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
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/samio.c:105:15: note: in expansion of macro 'FREEMEMORY'
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
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/samio.c:112:21: note: in expansion of macro 'FREEMEMORY'
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
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/samio.c:113:21: note: in expansion of macro 'FREEMEMORY'
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
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/samio.c:114:21: note: in expansion of macro 'FREEMEMORY'
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
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/samio.c:115:21: note: in expansion of macro 'FREEMEMORY'
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
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/samio.c:116:21: note: in expansion of macro 'FREEMEMORY'
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
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/samio.c:117:21: note: in expansion of macro 'FREEMEMORY'
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
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/samio.c:121:20: note: in expansion of macro 'FREEMEMORY'
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
if(samrec->tags) FREEMEMORY(NULL, samrec->tags);
^~
Building... library for source build/brendel.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/brendel.o libs/brendel.c
Building... library for source build/info.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/info.o libs/info.c
libs/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=]
sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d",
^~
libs/info.c:64:21: note: directive argument in the range [-2147481748, 2147483647]
sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libs/info.c:64:5: note: 'sprintf' output between 16 and 67 bytes into a destination of size 26
sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
wday_name[timeptr->tm_wday], mon_name[timeptr->tm_mon],
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
timeptr->tm_mday, timeptr->tm_hour, timeptr->tm_min,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
timeptr->tm_sec, 1900 + timeptr->tm_year);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libs/info.c: In function 'infomsg':
libs/info.c:64:50: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 12 [-Wformat-overflow=]
sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d",
^~
libs/info.c:64:21: note: directive argument in the range [-2147481748, 2147483647]
sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libs/info.c:64:5: note: 'sprintf' output between 16 and 67 bytes into a destination of size 26
sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
wday_name[timeptr->tm_wday], mon_name[timeptr->tm_mon],
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
timeptr->tm_mday, timeptr->tm_hour, timeptr->tm_min,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
timeptr->tm_sec, 1900 + timeptr->tm_year);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Building... library for source build/gzip.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/gzip.o libs/gzip.c
libs/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=]
sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d",
^~
libs/info.c:64:21: note: directive argument in the range [-2147481748, 2147483647]
sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libs/info.c:64:5: note: 'sprintf' output between 16 and 67 bytes into a destination of size 26
sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
wday_name[timeptr->tm_wday], mon_name[timeptr->tm_mon],
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
timeptr->tm_mday, timeptr->tm_hour, timeptr->tm_min,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
timeptr->tm_sec, 1900 + timeptr->tm_year);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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=]
fprintf(stderr, "common header has a length of %ld instead of %ld - not good.\n", bytesRead, sizeof(u_CommonHeader));
~~^ ~~~~~~~~~
%d
libs/gzip.c:41:71: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'unsigned int' [-Wformat=]
fprintf(stderr, "common header has a length of %ld instead of %ld - not good.\n", bytesRead, sizeof(u_CommonHeader));
~~^ ~~~~~~~~~~~~~~~~~~~~~~
%d
Building... library for source build/sufarray.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/sufarray.o libs/sufarray.c
Building... library for source build/fileBins.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/fileBins.o libs/fileBins.c
Building... library for source build/splitalign.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/splitalign.o libs/splitalign.c
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/sufarray.h:45,
from libs/sufarray.c:39:
libs/sufarray.c: In function 'destructSufArr':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/sufarray.c:613:5: note: in expansion of macro 'FREEMEMORY'
FREEMEMORY(space, arr->lcpctab);
^~~~~~~~~~
libs/sufarray.c:612:3: note: some parts of macro expansion are not guarded by this 'if' clause
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/sufarray.c:615:5: note: in expansion of macro 'FREEMEMORY'
FREEMEMORY(space, arr->inv_suftab);
^~~~~~~~~~
libs/sufarray.c:614:3: note: some parts of macro expansion are not guarded by this 'if' clause
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/sufarray.c:619:5: note: in expansion of macro 'FREEMEMORY'
FREEMEMORY(space, arr->idvtab);
^~~~~~~~~~
libs/sufarray.c:618:3: note: some parts of macro expansion are not guarded by this 'if' clause
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/sufarray.c:624:5: note: in expansion of macro 'FREEMEMORY'
FREEMEMORY(space, arr->suflink);
^~~~~~~~~~
libs/sufarray.c:620:3: note: some parts of macro expansion are not guarded by this 'if' clause
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/sufarray.c:627:5: note: in expansion of macro 'FREEMEMORY'
FREEMEMORY(space, arr->chldtab);
^~~~~~~~~~
libs/sufarray.c:626:3: note: some parts of macro expansion are not guarded by this 'if' clause
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/sufarray.c:629:5: note: in expansion of macro 'FREEMEMORY'
FREEMEMORY(space, arr->mdfive);
^~~~~~~~~~
libs/sufarray.c:628:3: note: some parts of macro expansion are not guarded by this 'if' clause
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/sufarray.c:631:5: note: in expansion of macro 'FREEMEMORY'
FREEMEMORY(space, arr->llvtab);
^~~~~~~~~~
libs/sufarray.c:630:3: note: some parts of macro expansion are not guarded by this 'if' clause
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/sufarray.c:636:5: note: in expansion of macro 'FREEMEMORY'
FREEMEMORY(space, arr->id);
^~~~~~~~~~
libs/sufarray.c:632:3: note: some parts of macro expansion are not guarded by this 'if' clause
if(arr->id != NULL)
^~
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/fileBins.c:901:18: note: in expansion of macro 'FREEMEMORY'
if(fileSort) FREEMEMORY(space, line);
^~~~~~~~~~
libs/fileBins.c:901:5: note: some parts of macro expansion are not guarded by this 'if' clause
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/splitalign.c:1323:25: note: in expansion of macro 'FREEMEMORY'
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
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/splitalign.c:1324:25: note: in expansion of macro 'FREEMEMORY'
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
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/splitalign.c:1325:26: note: in expansion of macro 'FREEMEMORY'
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
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/splitalign.c:1326:26: note: in expansion of macro 'FREEMEMORY'
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
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/splitalign.c:1565:27: note: in expansion of macro 'FREEMEMORY'
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
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/splitalign.c:1566:27: note: in expansion of macro 'FREEMEMORY'
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
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/splitalign.c:1567:28: note: in expansion of macro 'FREEMEMORY'
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
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/splitalign.c:1568:28: note: in expansion of macro 'FREEMEMORY'
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
if(rightseedno[1]) FREEMEMORY(space, rightseeds[1]);
^~
Building... library for source build/iupac.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/iupac.o libs/iupac.c
Building... library for source build/bitvectoralg.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/bitvectoralg.o libs/bitvectoralg.c
Building... library for source build/intervaltree.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/intervaltree.o libs/intervaltree.c
In file included from include/mathematics.h:117,
from libs/intervaltree.c:27:
libs/intervaltree.c: In function 'bl_intervaltreeDestruct':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/intervaltree.c:443:19: note: in expansion of macro 'FREEMEMORY'
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
if(root->ncoll) FREEMEMORY(NULL, root->collisions);
^~
Building... library for source build/haarz.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/haarz.o libs/haarz.c
Building... library for source build/manopt.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/manopt.o libs/manopt.c
Building... library for source build/mathematics.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/mathematics.o libs/mathematics.c
In file included from include/mathematics.h:117,
from libs/mathematics.c:38:
libs/mathematics.c: In function 'destructVector':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/mathematics.c:251:23: note: in expansion of macro 'FREEMEMORY'
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
if (v->elements) FREEMEMORY(space, v->elements);
^~
Building... library for source build/multicharseq.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/multicharseq.o libs/multicharseq.c
Building... library for source build/filebuffer.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/filebuffer.o libs/filebuffer.c
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/multicharseq.c:212:7: note: in expansion of macro 'FREEMEMORY'
FREEMEMORY(space, mseq->markpos);
^~~~~~~~~~
libs/multicharseq.c:211:2: note: some parts of macro expansion are not guarded by this 'if' clause
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/multicharseq.c:214:7: note: in expansion of macro 'FREEMEMORY'
FREEMEMORY(space, mseq->map);
^~~~~~~~~~
libs/multicharseq.c:213:2: note: some parts of macro expansion are not guarded by this 'if' clause
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/multicharseq.c:216:7: note: in expansion of macro 'FREEMEMORY'
FREEMEMORY(space, mseq->ref);
^~~~~~~~~~
libs/multicharseq.c:215:5: note: some parts of macro expansion are not guarded by this 'if' clause
if (mseq->ref != NULL)
^~
Building... library for source build/mapfrag.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/mapfrag.o libs/mapfrag.c
Building... library for source build/mappingqual.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/mappingqual.o libs/mappingqual.c
Building... library for source build/nw.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/nw.o libs/nw.c
Building... library for source build/alignment.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/alignment.o libs/alignment.c
Building... library for source build/matealign.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/matealign.o libs/matealign.c
In file included from include/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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/alignment.c:97:18: note: in expansion of macro 'FREEMEMORY'
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
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/alignment.c:98:18: note: in expansion of macro 'FREEMEMORY'
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
if(al->rmuseq) FREEMEMORY(NULL, al->u);
^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/locus.h:41,
from include/mapfrag.h:39,
from libs/matealign.c:32:
libs/matealign.c: In function 'bl_matealign':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/matealign.c:313:15: note: in expansion of macro 'FREEMEMORY'
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
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]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/matealign.c:314:15: note: in expansion of macro 'FREEMEMORY'
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
if(npos[1]) FREEMEMORY(NULL, spos[1]);
^~
Linking haarz
Linking segemehl
cc build/md5.o build/vstack.o build/queryalign.o build/annotation.o build/biofiles.o build/bitVector.o build/locus.o build/seqclip.o build/debug.o build/merge.o build/kdseed.o build/stack.o build/bamio.o build/vqueue.o build/aluruSort.o build/segemehl_helper.o build/bitArray.o build/samheader.o build/sw.o build/fileio.o build/kdchain.o build/vtprogressbar.o build/karlin.o build/bgzip.o build/gzidx.o build/portable_endian.o build/container.o build/bedfiles.o build/memory.o build/junctions.o build/pigeon.o build/radixsort.o build/sort.o build/match.o build/charsequence.o build/stringutils.o build/samio.o build/manout.o build/brendel.o build/info.o build/gzip.o build/sufarray.o build/fileBins.o build/splitalign.o build/iupac.o build/bitvectoralg.o build/intervaltree.o build/manopt.o build/mathematics.o build/multicharseq.o build/filebuffer.o build/mapfrag.o build/mappingqual.o build/nw.o build/alignment.o build/matealign.o build/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/biofiles.o build/bitVector.o build/locus.o build/seqclip.o build/debug.o build/merge.o build/kdseed.o build/stack.o build/bamio.o build/vqueue.o build/aluruSort.o build/segemehl_helper.o build/bitArray.o build/samheader.o build/sw.o build/fileio.o build/kdchain.o build/vtprogressbar.o build/karlin.o build/bgzip.o build/gzidx.o build/portable_endian.o build/container.o build/bedfiles.o build/memory.o build/junctions.o build/pigeon.o build/radixsort.o build/sort.o build/match.o build/charsequence.o build/stringutils.o build/samio.o build/manout.o build/brendel.o build/info.o build/gzip.o build/sufarray.o build/fileBins.o build/splitalign.o build/iupac.o build/bitvectoralg.o build/intervaltree.o build/manopt.o build/mathematics.o build/multicharseq.o build/filebuffer.o build/mapfrag.o build/mappingqual.o build/nw.o build/alignment.o build/matealign.o build/segemehl.o -o ./segemehl.x -lm -lpthread -lz -lncurses -L libs -lform -lmenu -L/usr/local/lib/ `pkg-config --libs htslib` -Wl,-z,relro -Wl,-z,now
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_auto_install -a
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
mv segemehl.x segemehl
mv haarz.x haarz
find . -name "*.x"
dh_install
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/segemehl/usr/bin/haarz debian/segemehl/usr/bin/segemehl were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/segemehl/usr/bin/haarz debian/segemehl/usr/bin/segemehl were not linked against libncurses.so.6 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/segemehl/usr/bin/haarz debian/segemehl/usr/bin/segemehl were not linked against libtinfo.so.6 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/segemehl/usr/bin/haarz debian/segemehl/usr/bin/segemehl were not linked against libform.so.6 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/segemehl/usr/bin/haarz debian/segemehl/usr/bin/segemehl were not linked against libmenu.so.6 (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-dbgsym' in '../segemehl-dbgsym_0.3.4-1_armhf.deb'.
dpkg-deb: building package 'segemehl' in '../segemehl_0.3.4-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../segemehl_0.3.4-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2019-01-17T06:38:48Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
segemehl_0.3.4-1_armhf.changes:
-------------------------------
Format: 1.8
Date: Fri, 11 Jan 2019 22:52:52 +0100
Source: segemehl
Binary: segemehl
Architecture: armhf
Version: 0.3.4-1
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
segemehl - short read mapping with gaps
Changes:
segemehl (0.3.4-1) unstable; urgency=medium
.
* New upstream version
* debhelper 12
* Standards-Version: 4.3.0
Checksums-Sha1:
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b187830856f2ec525fb83155aaba2f7b98efe69a 5275 segemehl_0.3.4-1_armhf.buildinfo
e4f46f9f33d2b0479319a68671586bf8a6459682 234104 segemehl_0.3.4-1_armhf.deb
Checksums-Sha256:
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138a97114d88f3ffb60c166a7f7440714f1eccf46fde92a5b34a79ad7397abe5 5275 segemehl_0.3.4-1_armhf.buildinfo
08c19ad01e733fd1442a41603f089a692bb6eb7afaf5bf4d80c4aee55ef432cd 234104 segemehl_0.3.4-1_armhf.deb
Files:
596c4ab43827638d171119db59a55825 1475816 debug optional segemehl-dbgsym_0.3.4-1_armhf.deb
b992754f4f83d399517a012f0d51c468 5275 science optional segemehl_0.3.4-1_armhf.buildinfo
592334163fb5e882cea87826bbf5a74b 234104 science optional segemehl_0.3.4-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
segemehl-dbgsym_0.3.4-1_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 1475816 bytes: control archive=648 bytes.
416 bytes, 12 lines control
300 bytes, 3 lines md5sums
Package: segemehl-dbgsym
Source: segemehl
Version: 0.3.4-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1604
Depends: segemehl (= 0.3.4-1)
Section: debug
Priority: optional
Description: debug symbols for segemehl
Build-Ids: 49969ec6642dcb710b3e53866edd48df3920e818 6e182cf0bfff147448ead1cd117ed35ea45ac995
drwxr-xr-x root/root 0 2019-01-11 21:52 ./
drwxr-xr-x root/root 0 2019-01-11 21:52 ./usr/
drwxr-xr-x root/root 0 2019-01-11 21:52 ./usr/lib/
drwxr-xr-x root/root 0 2019-01-11 21:52 ./usr/lib/debug/
drwxr-xr-x root/root 0 2019-01-11 21:52 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2019-01-11 21:52 ./usr/lib/debug/.build-id/49/
-rw-r--r-- root/root 790792 2019-01-11 21:52 ./usr/lib/debug/.build-id/49/969ec6642dcb710b3e53866edd48df3920e818.debug
drwxr-xr-x root/root 0 2019-01-11 21:52 ./usr/lib/debug/.build-id/6e/
-rw-r--r-- root/root 793268 2019-01-11 21:52 ./usr/lib/debug/.build-id/6e/182cf0bfff147448ead1cd117ed35ea45ac995.debug
drwxr-xr-x root/root 0 2019-01-11 21:52 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2019-01-11 21:52 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 43160 2019-01-11 21:52 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/segemehl.debug
drwxr-xr-x root/root 0 2019-01-11 21:52 ./usr/share/
drwxr-xr-x root/root 0 2019-01-11 21:52 ./usr/share/doc/
lrwxrwxrwx root/root 0 2019-01-11 21:52 ./usr/share/doc/segemehl-dbgsym -> segemehl
segemehl_0.3.4-1_armhf.deb
--------------------------
new Debian package, version 2.0.
size 234104 bytes: control archive=1364 bytes.
1653 bytes, 29 lines control
374 bytes, 6 lines md5sums
Package: segemehl
Version: 0.3.4-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1065
Depends: libc6 (>= 2.23), libhts2 (>= 1.4.1), libncurses6 (>= 6), libtinfo6 (>= 6), zlib1g (>= 1:1.2.2.4)
Section: science
Priority: optional
Homepage: http://www.bioinf.uni-leipzig.de/Software/segemehl/
Description: short read mapping with gaps
Segemehl is a software to map short sequencer reads to reference
genomes. Segemehl implements a matching strategy based on enhanced
suffix arrays (ESA). Segemehl accepts fasta and fastq queries (gzip’ed
and bgzip'ed). In addition to the alignment of reads from standard DNA-
and RNA-seq protocols, it also allows the mapping of bisulfite converted
reads (Lister and Cokus) and implements a split read mapping strategy.
The output of segemehl is a SAM or BAM formatted alignment file. In the
case of split-read mapping, additional BED files are written to the
disc. These BED files may be summarized with the postprocessing tool
haarz. In the case of the alignment of bisulfite converted reads, raw
methylation rates may also be called with haarz.
.
In brief, for each suffix of a read, segemehl aims to find the
best-scoring seed. Seeds might contain insertions, deletions, and
mismatches (differences). The number of differences allowed within a
single seed is user-controlled and is crucial for the runtime of the
program. Subsequently, seeds that undercut the user-defined E-value are
passed on to an exact semi-global alignment procedure. Finally, reads
with a minimum accuracy of percent are reported to the user.
drwxr-xr-x root/root 0 2019-01-11 21:52 ./
drwxr-xr-x root/root 0 2019-01-11 21:52 ./usr/
drwxr-xr-x root/root 0 2019-01-11 21:52 ./usr/bin/
-rwxr-xr-x root/root 534772 2019-01-11 21:52 ./usr/bin/haarz
-rwxr-xr-x root/root 538936 2019-01-11 21:52 ./usr/bin/segemehl
drwxr-xr-x root/root 0 2019-01-11 21:52 ./usr/share/
drwxr-xr-x root/root 0 2019-01-11 21:52 ./usr/share/doc/
drwxr-xr-x root/root 0 2019-01-11 21:52 ./usr/share/doc/segemehl/
-rw-r--r-- root/root 266 2019-01-11 21:52 ./usr/share/doc/segemehl/changelog.Debian.gz
-rw-r--r-- root/root 1009 2019-01-11 21:52 ./usr/share/doc/segemehl/copyright
drwxr-xr-x root/root 0 2019-01-11 21:52 ./usr/share/man/
drwxr-xr-x root/root 0 2019-01-11 21:52 ./usr/share/man/man1/
-rw-r--r-- root/root 505 2019-01-11 21:52 ./usr/share/man/man1/haarz.1.gz
-rw-r--r-- root/root 2427 2019-01-11 21:52 ./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: 15580
Build-Time: 122
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 361
Job: segemehl_0.3.4-1
Machine Architecture: armhf
Package: segemehl
Package-Time: 537
Source-Version: 0.3.4-1
Space: 15580
Status: successful
Version: 0.3.4-1
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Finished at 2019-01-17T06:38:48Z
Build needed 00:08:57, 15580k disc space