libgclib →
0.12.7+ds-5 →
armhf → 2022-11-11 06:50:26
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| libgclib 0.12.7+ds-5 (armhf) Fri, 11 Nov 2022 06:45:24 +0000 |
+==============================================================================+
Package: libgclib
Version: 0.12.7+ds-5
Source Version: 0.12.7+ds-5
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-8eb01ffd-526a-465d-bec3-5338aa518ee4' with '<<CHROOT>>'
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| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [13.4 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [14.3 MB]
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Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: http://172.17.4.1/private/dists/bookworm-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
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| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'libgclib' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/libgclib.git
Please use:
git clone https://salsa.debian.org/med-team/libgclib.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 274 kB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main libgclib 0.12.7+ds-5 (dsc) [2331 B]
Get:2 http://172.17.4.1/private bookworm-staging/main libgclib 0.12.7+ds-5 (tar) [257 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main libgclib 0.12.7+ds-5 (diff) [14.9 kB]
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Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/libgclib-RQ7o4A/libgclib-0.12.7+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/libgclib-RQ7o4A' with '<<BUILDDIR>>'
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| 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-Wz8wbz/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-Wz8wbz/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-Wz8wbz/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-Wz8wbz/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-Wz8wbz/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-Wz8wbz/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-Wz8wbz/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-Wz8wbz/apt_archive ./ Packages [432 B]
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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:
krb5-locales libpam-cap libperl5.34 netbase perl-modules-5.34 sensible-utils
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 55 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-Wz8wbz/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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Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
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Arch check ok (armhf included in any)
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| Install package build dependencies |
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Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), d-shlibs
Filtered Build-Depends: debhelper-compat (= 13), d-shlibs
dpkg-deb: building package 'sbuild-build-depends-libgclib-dummy' in '/<<BUILDDIR>>/resolver-Wz8wbz/apt_archive/sbuild-build-depends-libgclib-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-libgclib-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-Wz8wbz/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-Wz8wbz/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-Wz8wbz/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-Wz8wbz/apt_archive ./ Sources [499 B]
Get:5 copy:/<<BUILDDIR>>/resolver-Wz8wbz/apt_archive ./ Packages [577 B]
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Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install libgclib 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:
krb5-locales libpam-cap libperl5.34 netbase perl-modules-5.34
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils d-shlibs debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1
libfile-stripnondeterminism-perl libicu71 libmagic-mgc libmagic1
libpipeline1 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db
po-debconf
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils d-shlibs debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1
libfile-stripnondeterminism-perl libicu71 libmagic-mgc libmagic1
libpipeline1 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db
po-debconf sbuild-build-depends-libgclib-dummy
0 upgraded, 31 newly installed, 0 to remove and 55 not upgraded.
Need to get 17.9 MB of archives.
After this operation, 69.7 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-Wz8wbz/apt_archive ./ sbuild-build-depends-libgclib-dummy 0.invalid.0 [860 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-8 [793 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38.1-1.1 [78.2 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.6-3 [34.3 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.11.0-1 [1299 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-4 [295 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-4 [120 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-4 [65.8 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-9 [171 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.19-1 [260 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-9 [510 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf d-shlibs all 0.104 [18.6 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.10.1 [79.9 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-4 [526 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.187-2+rpi2 [177 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14+20220924-2 [93.1 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf libicu71 armhf 71.1-3 [8855 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1 [591 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-9 [1220 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.10.1 [940 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libxml2:armhf (2.9.14+dfsg-1) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
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Setting up groff-base (1.22.4-8) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.11.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.10.1) ...
Setting up sbuild-build-depends-libgclib-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.35-2+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-187-generic armhf (armv8l)
Toolchain package versions: binutils_2.39-6+rpi1 dpkg-dev_1.21.9+rpi1 g++-12_12.2.0-3+rpi1 gcc-12_12.2.0-3+rpi1 libc6-dev_2.35-2+rpi1 libstdc++-12-dev_12.2.0-3+rpi1 libstdc++6_12.2.0-3+rpi1 linux-libc-dev_5.19.6-1+rpi1
Package versions: adduser_3.129 apt_2.5.3 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-9 autotools-dev_20220109.1 base-files_12.3+rpi1 base-passwd_3.6.1 bash_5.2~rc2-2 binutils_2.39-6+rpi1 binutils-arm-linux-gnueabihf_2.39-6+rpi1 binutils-common_2.39-6+rpi1 bsdextrautils_2.38.1-1.1 bsdutils_1:2.38.1-1.1 build-essential_12.9 bzip2_1.0.8-5+b2 coreutils_9.1-1 cpp_4:12.2.0-1+rpi1 cpp-12_12.2.0-3+rpi1 d-shlibs_0.104 dash_0.5.11+git20210903+057cd650a4ed-9 debconf_1.5.79 debhelper_13.10.1 debianutils_5.7-0.3 dh-autoreconf_20 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-1 dirmngr_2.2.39-1 dpkg_1.21.9+rpi1 dpkg-dev_1.21.9+rpi1 dwz_0.14+20220924-2 e2fsprogs_1.46.6~rc1-1 fakeroot_1.29-1 file_1:5.41-4 findutils_4.9.0-3 g++_4:12.2.0-1+rpi1 g++-12_12.2.0-3+rpi1 gcc_4:12.2.0-1+rpi1 gcc-12_12.2.0-3+rpi1 gcc-12-base_12.2.0-3+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-9 gettext-base_0.21-9 gnupg_2.2.39-1 gnupg-l10n_2.2.39-1 gnupg-utils_2.2.39-1 gpg_2.2.39-1 gpg-agent_2.2.39-1 gpg-wks-client_2.2.39-1 gpg-wks-server_2.2.39-1 gpgconf_2.2.39-1 gpgsm_2.2.39-1 gpgv_2.2.39-1 grep_3.7-1 groff-base_1.22.4-8 gzip_1.12-1 hostname_3.23 init-system-helpers_1.64 intltool-debian_0.35.0+20060710.6 iputils-ping_3:20211215-1 krb5-locales_1.20-1 libacl1_2.3.1-1 libapt-pkg6.0_2.5.3 libarchive-zip-perl_1.68-1 libasan8_12.2.0-3+rpi1 libassuan0_2.5.5-4 libatomic1_12.2.0-3+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.7-1.1 libaudit1_1:3.0.7-1.1 libbinutils_2.39-6+rpi1 libblkid1_2.38.1-1.1 libbz2-1.0_1.0.8-5+b2 libc-bin_2.35-2+rpi1 libc-dev-bin_2.35-2+rpi1 libc6_2.35-2+rpi1 libc6-dev_2.35-2+rpi1 libcap-ng0_0.8.3-1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_12.2.0-3+rpi1 libcom-err2_1.46.6~rc1-1 libcrypt-dev_1:4.4.28-2 libcrypt1_1:4.4.28-2 libctf-nobfd0_2.39-6+rpi1 libctf0_2.39-6+rpi1 libdb5.3_5.3.28+dfsg1-0.10 libdebconfclient0_0.264 libdebhelper-perl_13.10.1 libdpkg-perl_1.21.9+rpi1 libelf1_0.187-2+rpi2 libext2fs2_1.46.6~rc1-1 libfakeroot_1.29-1 libffi8_3.4.2-4 libfile-stripnondeterminism-perl_1.13.0-1 libgcc-12-dev_12.2.0-3+rpi1 libgcc-s1_12.2.0-3+rpi1 libgcrypt20_1.10.1-2+b2 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgmp10_2:6.2.1+dfsg1-1.1 libgnutls30_3.7.8-2 libgomp1_12.2.0-3+rpi1 libgpg-error0_1.45-2 libgssapi-krb5-2_1.20-1 libhogweed6_3.8.1-2 libicu71_71.1-3 libidn2-0_2.3.3-1 libisl23_0.25-1 libk5crypto3_1.20-1 libkeyutils1_1.6.3-1 libkrb5-3_1.20-1 libkrb5support0_1.20-1 libksba8_1.6.0-3 libldap-2.5-0_2.5.13+dfsg-2+rpi1 liblz4-1_1.9.4-1+rpi1 liblzma5_5.2.5-2.1 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmount1_2.38.1-1.1 libmpc3_1.2.1-2 libmpfr6_4.1.0-3 libncursesw6_6.3+20220423-2 libnettle8_3.8.1-2 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.1-1 libpam-cap_1:2.44-1 libpam-modules_1.5.2-5 libpam-modules-bin_1.5.2-5 libpam-runtime_1.5.2-5 libpam0g_1.5.2-5 libpcre2-8-0_10.40-1+b2 libpcre3_2:8.39-14 libperl5.34_5.34.0-5 libperl5.36_5.36.0-4 libpipeline1_1.5.6-3 libreadline8_8.2-1 libsasl2-2_2.1.28+dfsg-8 libsasl2-modules-db_2.1.28+dfsg-8 libseccomp2_2.5.4-1+rpi1 libselinux1_3.4-1 libsemanage-common_3.4-1 libsemanage2_3.4-1 libsepol1_3.1-1 libsepol2_3.4-2 libsmartcols1_2.38.1-1.1 libsqlite3-0_3.39.4-1 libss2_1.46.6~rc1-1 libssl1.1_1.1.1o-1 libssl3_3.0.5-4 libstdc++-12-dev_12.2.0-3+rpi1 libstdc++6_12.2.0-3+rpi1 libsub-override-perl_0.09-4 libsystemd0_251.5-1+rpi1 libtasn1-6_4.19.0-2 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-4 libubsan1_12.2.0-3+rpi1 libuchardet0_0.0.7-1 libudev1_251.5-1+rpi1 libunistring2_1.0-2 libuuid1_2.38.1-1.1 libxml2_2.9.14+dfsg-1 libxxhash0_0.8.1-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.19.6-1+rpi1 login_1:4.12.3+dfsg1-1 logsave_1.46.6~rc1-1 lsb-base_11.4+rpi1 m4_1.4.19-1 make_4.3-4.1 man-db_2.11.0-1 mawk_1.3.4.20200120-3.1 mount_2.38.1-1.1 nano_6.4-1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 netbase_6.3 passwd_1:4.12.3+dfsg1-1 patch_2.7.6-7 perl_5.36.0-4 perl-base_5.36.0-4 perl-modules-5.34_5.34.0-5 perl-modules-5.36_5.36.0-4 pinentry-curses_1.2.0-2 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.2-1 rpcsvc-proto_1.4.2-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-libgclib-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sgml-base_1.31 sysvinit-utils_3.05-6 tar_1.34+dfsg-1 tzdata_2022d-1 util-linux_2.38.1-1.1 util-linux-extra_2.38.1-1.1 xz-utils_5.2.5-2.1 zlib1g_1:1.2.11.dfsg-4.1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.93ICTtgw/trustedkeys.kbx': General error
gpgv: Signature made Tue Nov 8 20:32:16 2022 UTC
gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv: issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./libgclib_0.12.7+ds-5.dsc
dpkg-source: info: extracting libgclib in /<<BUILDDIR>>/libgclib-0.12.7+ds
dpkg-source: info: unpacking libgclib_0.12.7+ds.orig.tar.gz
dpkg-source: info: unpacking libgclib_0.12.7+ds-5.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying autoconf.patch
dpkg-source: info: applying CVE-2021-42006.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-8eb01ffd-526a-465d-bec3-5338aa518ee4
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package libgclib
dpkg-buildpackage: info: source version 0.12.7+ds-5
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/libgclib-0.12.7+ds'
if [ -r Makefile -a -r Makefile.am ]; then dh_auto_clean; fi
rm -f Makefile Makefile.in aclocal.m4 config.h.in configure debian/autoreconf.after debian/autoreconf.before
find . -name "*.o" -delete
make[1]: Leaving directory '/<<BUILDDIR>>/libgclib-0.12.7+ds'
dh_clean
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
aclocal: warning: couldn't open directory 'config': No such file or directory
libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'config'.
libtoolize: copying file 'config/ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'config'.
libtoolize: copying file 'config/libtool.m4'
libtoolize: copying file 'config/ltoptions.m4'
libtoolize: copying file 'config/ltsugar.m4'
libtoolize: copying file 'config/ltversion.m4'
libtoolize: copying file 'config/lt~obsolete.m4'
libtoolize: Consider adding '-I config' to ACLOCAL_AMFLAGS in Makefile.am.
configure.ac:30: warning: The macro `AC_PROG_LIBTOOL' is obsolete.
configure.ac:30: You should run autoupdate.
config/libtool.m4:100: AC_PROG_LIBTOOL is expanded from...
configure.ac:30: the top level
configure.ac:51: warning: The macro `AC_HEADER_STDC' is obsolete.
configure.ac:51: You should run autoupdate.
./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from...
configure.ac:51: the top level
configure.ac:30: installing 'config/compile'
configure.ac:30: installing 'config/config.guess'
configure.ac:30: installing 'config/config.sub'
configure.ac:18: installing 'config/install-sh'
configure.ac:18: installing 'config/missing'
Makefile.am: installing 'config/depcomp'
dh_auto_configure -a
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether UID '107' is supported by ustar format... yes
checking whether GID '112' is supported by ustar format... yes
checking how to create a ustar tar archive... gnutar
checking whether ln -s works... yes
checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking how to print strings... printf
checking whether make supports the include directive... yes (GNU style)
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 1572864
checking how to convert arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop
checking how to convert arm-unknown-linux-gnueabihf file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for file... file
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for g++... g++
checking whether the compiler supports GNU C++... yes
checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... none needed
checking dependency style of g++... none
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
./configure: line 16912: AX_CXXFLAGS: command not found
checking for egrep... (cached) /bin/grep -E
checking for stdlib.h... (cached) yes
checking whether make sets $(MAKE)... (cached) yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating libgclib.pc
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
dh_auto_build -a
make -j4
make[1]: Entering directory '/<<BUILDDIR>>/libgclib-0.12.7+ds'
make all-am
make[2]: Entering directory '/<<BUILDDIR>>/libgclib-0.12.7+ds'
g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o mdtest.o mdtest.cpp
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-codons.lo `test -f 'codons.cpp' || echo './'`codons.cpp
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GAlnExtend.lo `test -f 'GAlnExtend.cpp' || echo './'`GAlnExtend.cpp
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GapAssem.lo `test -f 'GapAssem.cpp' || echo './'`GapAssem.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c codons.cpp -fPIC -DPIC -o .libs/libgclib_la-codons.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GAlnExtend.cpp -fPIC -DPIC -o .libs/libgclib_la-GAlnExtend.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GapAssem.cpp -fPIC -DPIC -o .libs/libgclib_la-GapAssem.o
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GArgs.lo `test -f 'GArgs.cpp' || echo './'`GArgs.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c codons.cpp -o libgclib_la-codons.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GArgs.cpp -fPIC -DPIC -o .libs/libgclib_la-GArgs.o
GapAssem.cpp: In member function ‘GASeq::refineClipping(GDynArray<char>&, int, bool)’:
GapAssem.cpp:239:23: warning: ‘gseq’ may be used uninitialized [-Wmaybe-uninitialized]
239 | gseq[allocsize] = 0;
| ^
GapAssem.cpp:212:15: note: ‘gseq’ was declared here
212 | char* gseq;
| ^~~~
GapAssem.cpp:366:46: warning: ‘gxpos’ may be used uninitialized [-Wmaybe-uninitialized]
366 | clipL = gxpos[bestpos];
| ^
GapAssem.cpp:236:14: note: ‘gxpos’ was declared here
236 | int* gxpos; //mapping of positions from gseq to seq
| ^~~~~
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GBase.lo `test -f 'GBase.cpp' || echo './'`GBase.cpp
GAlnExtend.cpp: In function ‘color_fg(int, _IO_FILE*)’:
GAlnExtend.cpp:13:35: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 4 [-Wformat-overflow=]
13 | sprintf((char *)(&COLOR_buf[2]),"%dm",c+30);
| ^~
In function ‘color_fg(int, _IO_FILE*)’,
inlined from ‘color_fg(int, _IO_FILE*)’ at GAlnExtend.cpp:11:6:
GAlnExtend.cpp:13:34: note: directive argument in the range [-2147483618, 2147483647]
13 | sprintf((char *)(&COLOR_buf[2]),"%dm",c+30);
| ^~~~~
In file included from /usr/include/stdio.h:906,
from GBase.h:63,
from GAlnExtend.h:6,
from GAlnExtend.cpp:1:
In function ‘sprintf’,
inlined from ‘color_fg(int, _IO_FILE*)’ at GAlnExtend.cpp:13:9,
inlined from ‘color_fg(int, _IO_FILE*)’ at GAlnExtend.cpp:11:6:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 3 and 13 bytes into a destination of size 4
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
GAlnExtend.cpp: In function ‘color_bg(int, _IO_FILE*)’:
GAlnExtend.cpp:19:35: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 4 [-Wformat-overflow=]
19 | sprintf((char *)(&COLOR_buf[2]),"%dm",c+40);
| ^~
In function ‘color_bg(int, _IO_FILE*)’,
inlined from ‘color_bg(int, _IO_FILE*)’ at GAlnExtend.cpp:17:6:
GAlnExtend.cpp:19:34: note: directive argument in the range [-2147483608, 2147483647]
19 | sprintf((char *)(&COLOR_buf[2]),"%dm",c+40);
| ^~~~~
In function ‘sprintf’,
inlined from ‘color_bg(int, _IO_FILE*)’ at GAlnExtend.cpp:19:9,
inlined from ‘color_bg(int, _IO_FILE*)’ at GAlnExtend.cpp:17:6:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 3 and 13 bytes into a destination of size 4
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GBase.cpp -fPIC -DPIC -o .libs/libgclib_la-GBase.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GArgs.cpp -o libgclib_la-GArgs.o >/dev/null 2>&1
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gcdb.lo `test -f 'gcdb.cpp' || echo './'`gcdb.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GapAssem.cpp -o libgclib_la-GapAssem.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GAlnExtend.cpp -o libgclib_la-GAlnExtend.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gcdb.cpp -fPIC -DPIC -o .libs/libgclib_la-gcdb.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GBase.cpp -o libgclib_la-GBase.o >/dev/null 2>&1
gcdb.cpp: In function ‘unsigned int gcdb_strlen(const char*)’:
gcdb.cpp:102:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
102 | register char *t;
| ^
gcdb.cpp: In constructor ‘GCdbRead::GCdbRead(int)’:
gcdb.cpp:809:13: warning: comparing the result of pointer addition ‘(x + 1)’ and NULL [-Waddress]
809 | if (x + 1) {
| ~~^~~
gcdb.cpp: In constructor ‘GCdbRead::GCdbRead(char*)’:
gcdb.cpp:843:13: warning: comparing the result of pointer addition ‘(x + 1)’ and NULL [-Waddress]
843 | if (x + 1) {
| ~~^~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gcdb.cpp -o libgclib_la-gcdb.o >/dev/null 2>&1
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GCdbYank.lo `test -f 'GCdbYank.cpp' || echo './'`GCdbYank.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GCdbYank.cpp -fPIC -DPIC -o .libs/libgclib_la-GCdbYank.o
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gdna.lo `test -f 'gdna.cpp' || echo './'`gdna.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gdna.cpp -fPIC -DPIC -o .libs/libgclib_la-gdna.o
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GFaSeqGet.lo `test -f 'GFaSeqGet.cpp' || echo './'`GFaSeqGet.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GCdbYank.cpp -o libgclib_la-GCdbYank.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GFaSeqGet.cpp -fPIC -DPIC -o .libs/libgclib_la-GFaSeqGet.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gdna.cpp -o libgclib_la-gdna.o >/dev/null 2>&1
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GFastaIndex.lo `test -f 'GFastaIndex.cpp' || echo './'`GFastaIndex.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GFastaIndex.cpp -fPIC -DPIC -o .libs/libgclib_la-GFastaIndex.o
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gff.lo `test -f 'gff.cpp' || echo './'`gff.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gff.cpp -fPIC -DPIC -o .libs/libgclib_la-gff.o
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gsocket.lo `test -f 'gsocket.cpp' || echo './'`gsocket.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gsocket.cpp -fPIC -DPIC -o .libs/libgclib_la-gsocket.o
In file included from gff.cpp:1:
gff.h:242:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
242 | struct {
| ^
gff.h:245:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
245 | struct {
| ^
gff.h:343:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
343 | struct {
| ^
gff.h:706:14: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
706 | struct {
| ^
gff.h:1165:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
1165 | struct {
| ^
gff.cpp: In constructor ‘GffLine::GffLine(GffReader*, const char*)’:
gff.cpp:426:19: warning: unknown escape sequence: '\%'
426 | GMessage("Warning: unexpected tab character in last column, line truncated:\n\%s\n",l);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GFaSeqGet.cpp -o libgclib_la-GFaSeqGet.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gsocket.cpp -o libgclib_la-gsocket.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GFastaIndex.cpp -o libgclib_la-GFastaIndex.o >/dev/null 2>&1
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gstopwatch.lo `test -f 'gstopwatch.cpp' || echo './'`gstopwatch.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gstopwatch.cpp -fPIC -DPIC -o .libs/libgclib_la-gstopwatch.o
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GStr.lo `test -f 'GStr.cpp' || echo './'`GStr.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gstopwatch.cpp -o libgclib_la-gstopwatch.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GStr.cpp -fPIC -DPIC -o .libs/libgclib_la-GStr.o
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GThreads.lo `test -f 'GThreads.cpp' || echo './'`GThreads.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GThreads.cpp -fPIC -DPIC -o .libs/libgclib_la-GThreads.o
GStr.cpp: In function ‘GStr::new_data(unsigned int, unsigned int)’:
GStr.cpp:23:22: warning: ‘data’ may be used uninitialized [-Wmaybe-uninitialized]
23 | data->length = len;
| ~~~~~~~~~~~~~^~~~~
GStr.cpp:20:15: note: ‘data’ was declared here
20 | Data* data;
| ^~~~
GStr.cpp: In function ‘GStr::new_data(char const*, unsigned int)’:
GStr.cpp:40:31: warning: ‘data’ may be used uninitialized [-Wmaybe-uninitialized]
40 | if (len) strcpy(data->chars, str);
| ~~~~~~^~~~~
GStr.cpp:38:15: note: ‘data’ was declared here
38 | Data* data;
| ^~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GThreads.cpp -o libgclib_la-GThreads.o >/dev/null 2>&1
In file included from gff.h:6:
GBase.h: In member function ‘BEDLine::BEDLine(GffReader*, char const*)’:
GBase.h:176:28: warning: ‘blen’ may be used uninitialized [-Wmaybe-uninitialized]
176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \
| ^~
gff.cpp:241:18: note: ‘blen’ was declared here
241 | char** blen;
| ^~~~
gff.cpp:242:18: warning: ‘bstart’ may be used uninitialized [-Wmaybe-uninitialized]
242 | char** bstart;
| ^~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GStr.cpp -o libgclib_la-GStr.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gff.cpp -o libgclib_la-gff.o >/dev/null 2>&1
/bin/bash ./libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -version-info 3:0 -lpthread -Wl,-z,relro -Wl,-z,now -Wl,-flto -o libgclib.la -rpath /usr/lib/arm-linux-gnueabihf libgclib_la-codons.lo libgclib_la-GAlnExtend.lo libgclib_la-GapAssem.lo libgclib_la-GArgs.lo libgclib_la-GBase.lo libgclib_la-gcdb.lo libgclib_la-GCdbYank.lo libgclib_la-gdna.lo libgclib_la-GFaSeqGet.lo libgclib_la-GFastaIndex.lo libgclib_la-gff.lo libgclib_la-gsocket.lo libgclib_la-gstopwatch.lo libgclib_la-GStr.lo libgclib_la-GThreads.lo
libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/12/crtbeginS.o .libs/libgclib_la-codons.o .libs/libgclib_la-GAlnExtend.o .libs/libgclib_la-GapAssem.o .libs/libgclib_la-GArgs.o .libs/libgclib_la-GBase.o .libs/libgclib_la-gcdb.o .libs/libgclib_la-GCdbYank.o .libs/libgclib_la-gdna.o .libs/libgclib_la-GFaSeqGet.o .libs/libgclib_la-GFastaIndex.o .libs/libgclib_la-gff.o .libs/libgclib_la-gsocket.o .libs/libgclib_la-gstopwatch.o .libs/libgclib_la-GStr.o .libs/libgclib_la-GThreads.o -lpthread -L/usr/lib/gcc/arm-linux-gnueabihf/12 -L/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/12/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/12/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/crtn.o -g -O2 -fstack-protector-strong -flto -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-flto -Wl,-soname -Wl,libgclib.so.3 -o .libs/libgclib.so.3.0.0
lto-wrapper: warning: using serial compilation of 5 LTRANS jobs
lto-wrapper: note: see the '-flto' option documentation for more information
In member function 'setCapacity',
inlined from 'Grow' at GVec.hh:323:13,
inlined from 'Add.constprop.isra' at GVec.hh:370:29:
GVec.hh:107:24: warning: argument 1 value '4294967295' exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
107 | fArray=new OBJ[NewCapacity];
| ^
/usr/include/c++/12/new: In member function 'Add.constprop.isra':
/usr/include/c++/12/new:128:26: note: in a call to allocation function 'operator new []' declared here
128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
| ^
libtool: link: (cd ".libs" && rm -f "libgclib.so.3" && ln -s "libgclib.so.3.0.0" "libgclib.so.3")
libtool: link: (cd ".libs" && rm -f "libgclib.so" && ln -s "libgclib.so.3.0.0" "libgclib.so")
libtool: link: ar cr .libs/libgclib.a libgclib_la-codons.o libgclib_la-GAlnExtend.o libgclib_la-GapAssem.o libgclib_la-GArgs.o libgclib_la-GBase.o libgclib_la-gcdb.o libgclib_la-GCdbYank.o libgclib_la-gdna.o libgclib_la-GFaSeqGet.o libgclib_la-GFastaIndex.o libgclib_la-gff.o libgclib_la-gsocket.o libgclib_la-gstopwatch.o libgclib_la-GStr.o libgclib_la-GThreads.o
libtool: link: ranlib .libs/libgclib.a
libtool: link: ( cd ".libs" && rm -f "libgclib.la" && ln -s "../libgclib.la" "libgclib.la" )
/bin/bash ./libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -Wl,-z,relro -Wl,-z,now -Wl,-flto -o mdtest mdtest.o libgclib.la
libtool: link: g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libgclib-0.12.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-flto -o .libs/mdtest mdtest.o ./.libs/libgclib.so
make[2]: Leaving directory '/<<BUILDDIR>>/libgclib-0.12.7+ds'
make[1]: Leaving directory '/<<BUILDDIR>>/libgclib-0.12.7+ds'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/libgclib-0.12.7+ds'
./mdtest 7TEST^BCT
7 matching bases
base mismatch [T]
base mismatch [E]
base mismatch [S]
base mismatch [T]
3 base(s) deletion [BCT]
make[1]: Leaving directory '/<<BUILDDIR>>/libgclib-0.12.7+ds'
create-stamp debian/debhelper-build-stamp
dh_prep -a
dh_auto_install -a
make -j1 install DESTDIR=/<<BUILDDIR>>/libgclib-0.12.7\+ds/debian/tmp AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/<<BUILDDIR>>/libgclib-0.12.7+ds'
make[2]: Entering directory '/<<BUILDDIR>>/libgclib-0.12.7+ds'
/bin/mkdir -p '/<<BUILDDIR>>/libgclib-0.12.7+ds/debian/tmp/usr/lib/arm-linux-gnueabihf'
/bin/bash ./libtool --mode=install /usr/bin/install -c libgclib.la '/<<BUILDDIR>>/libgclib-0.12.7+ds/debian/tmp/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/libgclib.so.3.0.0 /<<BUILDDIR>>/libgclib-0.12.7+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/libgclib.so.3.0.0
libtool: install: (cd /<<BUILDDIR>>/libgclib-0.12.7+ds/debian/tmp/usr/lib/arm-linux-gnueabihf && { ln -s -f libgclib.so.3.0.0 libgclib.so.3 || { rm -f libgclib.so.3 && ln -s libgclib.so.3.0.0 libgclib.so.3; }; })
libtool: install: (cd /<<BUILDDIR>>/libgclib-0.12.7+ds/debian/tmp/usr/lib/arm-linux-gnueabihf && { ln -s -f libgclib.so.3.0.0 libgclib.so || { rm -f libgclib.so && ln -s libgclib.so.3.0.0 libgclib.so; }; })
libtool: install: /usr/bin/install -c .libs/libgclib.lai /<<BUILDDIR>>/libgclib-0.12.7+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/libgclib.la
libtool: install: /usr/bin/install -c .libs/libgclib.a /<<BUILDDIR>>/libgclib-0.12.7+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/libgclib.a
libtool: install: chmod 644 /<<BUILDDIR>>/libgclib-0.12.7+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/libgclib.a
libtool: install: ranlib /<<BUILDDIR>>/libgclib-0.12.7+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/libgclib.a
libtool: warning: remember to run 'libtool --finish /usr/lib/arm-linux-gnueabihf'
/bin/mkdir -p '/<<BUILDDIR>>/libgclib-0.12.7+ds/debian/tmp/usr/bin'
/bin/bash ./libtool --mode=install /usr/bin/install -c mdtest '/<<BUILDDIR>>/libgclib-0.12.7+ds/debian/tmp/usr/bin'
libtool: warning: 'libgclib.la' has not been installed in '/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/mdtest /<<BUILDDIR>>/libgclib-0.12.7+ds/debian/tmp/usr/bin/mdtest
/bin/mkdir -p '/<<BUILDDIR>>/libgclib-0.12.7+ds/debian/tmp/usr/include'
/usr/bin/install -c -m 644 GAlnExtend.h GArgs.h GBam.h GBase.h GBitVec.h GCdbYank.h GFaSeqGet.h GFastaFile.h GFastaIndex.h GResUsage.h GStr.h GThreads.h GapAssem.h codons.h config.h gcdb.h gdimg.h gdna.h gff.h gsocket.h gstopwatch.h proc_mem.h wyhash.h xxhash.h GHash.hh GHashMap.hh GIntHash.hh GIntervalTree.hh GList.hh GVec.hh khashl.hh '/<<BUILDDIR>>/libgclib-0.12.7+ds/debian/tmp/usr/include'
/bin/mkdir -p '/<<BUILDDIR>>/libgclib-0.12.7+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig'
/usr/bin/install -c -m 644 libgclib.pc '/<<BUILDDIR>>/libgclib-0.12.7+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig'
make[2]: Leaving directory '/<<BUILDDIR>>/libgclib-0.12.7+ds'
make[1]: Leaving directory '/<<BUILDDIR>>/libgclib-0.12.7+ds'
debian/rules override_dh_install
make[1]: Entering directory '/<<BUILDDIR>>/libgclib-0.12.7+ds'
dh_install
d-shlibmove --commit \
--multiarch \
--devunversioned \
--exclude-la \
--movedev debian/tmp/usr/include usr \
--movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/arm-linux-gnueabihf/pkgconfig \
debian/tmp/usr/lib/*/*.so
Library package automatic movement utility
set -e
install -d -m 755 debian/libgclib-dev/usr/lib/arm-linux-gnueabihf
install -d -m 755 debian/libgclib3/usr/lib/arm-linux-gnueabihf
mv debian/tmp/usr/lib/arm-linux-gnueabihf/libgclib.a debian/libgclib-dev/usr/lib/arm-linux-gnueabihf
mv debian/tmp/usr/lib/arm-linux-gnueabihf/libgclib.so debian/libgclib-dev/usr/lib/arm-linux-gnueabihf
mv /<<BUILDDIR>>/libgclib-0.12.7+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/libgclib.so.3 debian/libgclib3/usr/lib/arm-linux-gnueabihf
mv /<<BUILDDIR>>/libgclib-0.12.7+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/libgclib.so.3.0.0 debian/libgclib3/usr/lib/arm-linux-gnueabihf
PKGDEV=libgclib-dev
PKGSHL=libgclib3
install -d -m 755 debian/libgclib-dev/usr
mv debian/tmp/usr/include debian/libgclib-dev/usr
install -d -m 755 debian/libgclib-dev/usr/lib/arm-linux-gnueabihf/pkgconfig
mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libgclib-dev/usr/lib/arm-linux-gnueabihf/pkgconfig
mkdir debian/libgclib-dev/usr/include/gclib
mv debian/libgclib-dev/usr/include/*.h* debian/libgclib-dev/usr/include/gclib
sed -i '/PACKAGE_NAME/d' debian/libgclib-dev/usr/include/gclib/config.h
# delete header files of not compiled C++ source files
find debian/libgclib-dev -name gdimg.h -delete
find debian/libgclib-dev -name GBam.h -delete
make[1]: Leaving directory '/<<BUILDDIR>>/libgclib-0.12.7+ds'
dh_installdocs -a
dh_installchangelogs -a
debian/rules override_dh_installexamples
make[1]: Entering directory '/<<BUILDDIR>>/libgclib-0.12.7+ds'
dh_installexamples
chmod a-x debian/libgclib-dev/usr/share/doc/libgclib-dev/examples/*
make[1]: Leaving directory '/<<BUILDDIR>>/libgclib-0.12.7+ds'
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: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/libgclib3/usr/lib/arm-linux-gnueabihf/libgclib.so.3.0.0 found in none of the libraries
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'libgclib-dev' in '../libgclib-dev_0.12.7+ds-5_armhf.deb'.
dpkg-deb: building package 'libgclib3' in '../libgclib3_0.12.7+ds-5_armhf.deb'.
dpkg-deb: building package 'libgclib3-dbgsym' in '../libgclib3-dbgsym_0.12.7+ds-5_armhf.deb'.
dpkg-genbuildinfo --build=any -O../libgclib_0.12.7+ds-5_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> -O../libgclib_0.12.7+ds-5_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2022-11-11T06:50:22Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
libgclib_0.12.7+ds-5_armhf.changes:
-----------------------------------
Format: 1.8
Date: Tue, 08 Nov 2022 21:07:26 +0100
Source: libgclib
Binary: libgclib-dev libgclib3 libgclib3-dbgsym
Architecture: armhf
Version: 0.12.7+ds-5
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
libgclib-dev - header files for Genome Code Lib (GCLib)
libgclib3 - C++ library to handle biological short sequence data
Changes:
libgclib (0.12.7+ds-5) unstable; urgency=medium
.
* d/control: add myself to uploaders.
* d/rules: add build option -ffat-lto-objects to restore usable code,
per lintian error no-code-sections.
* d/watch: fix github change; switch to git mode.
* d/control: declare compliance to standards version 4.6.1.
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Checksums-Sha256:
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Files:
c092ea55fcb2c0542f5b7880d6b110fc 263548 libdevel optional libgclib-dev_0.12.7+ds-5_armhf.deb
ed54a835fec4b258e89eb0355f76ff50 586124 debug optional libgclib3-dbgsym_0.12.7+ds-5_armhf.deb
a9a7ead2f85fc614ab4c90ad448fd32c 121560 libs optional libgclib3_0.12.7+ds-5_armhf.deb
567e89b680ab4b0c7cd5fd2b29f85a3a 6279 science optional libgclib_0.12.7+ds-5_armhf.buildinfo
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
libgclib-dev_0.12.7+ds-5_armhf.deb
----------------------------------
new Debian package, version 2.0.
size 263548 bytes: control archive=1980 bytes.
1229 bytes, 27 lines control
2195 bytes, 34 lines md5sums
Package: libgclib-dev
Source: libgclib
Version: 0.12.7+ds-5
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1113
Depends: libgclib3 (= 0.12.7+ds-5)
Section: libdevel
Priority: optional
Multi-Arch: same
Homepage: https://github.com/gpertea/gclib
Description: header files for Genome Code Lib (GCLib)
This is an eclectic gathering of (mostly) C++ code which upstream used
for some bioinformatics projects. The main idea is to provide
lean code and efficient data structures, trying to avoid too many code
dependencies of heavy libraries while minimizing production cycles (and
this also implies a decent compile/build time -- looking at you,
bloated configure scripts and lengthy compile times of Boost code or
other heavy C++ template code..).
.
This code was gathered even before the C++ STL had been fully adopted as
a cross-platform "standard". Since STL by itself is a bit heavier for
most of the C++ needs, it is preferred to use simpler&leaner C++ classes
or templates for basic strings, containers, basic algorithms etc.
.
Header files of Genome Code Lib. It is mainly known for being
used by StringTie but with its own release cycle.
drwxr-xr-x root/root 0 2022-11-08 20:07 ./
drwxr-xr-x root/root 0 2022-11-08 20:07 ./usr/
drwxr-xr-x root/root 0 2022-11-08 20:07 ./usr/include/
drwxr-xr-x root/root 0 2022-11-08 20:07 ./usr/include/gclib/
-rw-r--r-- root/root 25377 2022-11-08 20:07 ./usr/include/gclib/GAlnExtend.h
-rw-r--r-- root/root 4020 2022-11-08 20:07 ./usr/include/gclib/GArgs.h
-rw-r--r-- root/root 22908 2022-11-08 20:07 ./usr/include/gclib/GBase.h
-rw-r--r-- root/root 13820 2022-11-08 20:07 ./usr/include/gclib/GBitVec.h
-rw-r--r-- root/root 1952 2022-11-08 20:07 ./usr/include/gclib/GCdbYank.h
-rw-r--r-- root/root 10695 2022-11-08 20:07 ./usr/include/gclib/GFaSeqGet.h
-rw-r--r-- root/root 24292 2022-11-08 20:07 ./usr/include/gclib/GFastaFile.h
-rw-r--r-- root/root 2021 2022-11-08 20:07 ./usr/include/gclib/GFastaIndex.h
-rw-r--r-- root/root 16741 2022-11-08 20:07 ./usr/include/gclib/GHash.hh
-rw-r--r-- root/root 14220 2022-11-08 20:07 ./usr/include/gclib/GHashMap.hh
-rw-r--r-- root/root 12237 2022-11-08 20:07 ./usr/include/gclib/GIntHash.hh
-rw-r--r-- root/root 18091 2022-11-08 20:07 ./usr/include/gclib/GIntervalTree.hh
-rw-r--r-- root/root 21937 2022-11-08 20:07 ./usr/include/gclib/GList.hh
-rw-r--r-- root/root 1572 2022-11-08 20:07 ./usr/include/gclib/GResUsage.h
-rw-r--r-- root/root 9928 2022-11-08 20:07 ./usr/include/gclib/GStr.h
-rw-r--r-- root/root 24745 2022-11-08 20:07 ./usr/include/gclib/GThreads.h
-rw-r--r-- root/root 27190 2022-11-08 20:07 ./usr/include/gclib/GVec.hh
-rw-r--r-- root/root 15220 2022-11-08 20:07 ./usr/include/gclib/GapAssem.h
-rw-r--r-- root/root 1149 2022-11-08 20:07 ./usr/include/gclib/codons.h
-rw-r--r-- root/root 1905 2022-11-08 20:07 ./usr/include/gclib/config.h
-rw-r--r-- root/root 13832 2022-11-08 20:07 ./usr/include/gclib/gcdb.h
-rw-r--r-- root/root 435 2022-11-08 20:07 ./usr/include/gclib/gdna.h
-rw-r--r-- root/root 52083 2022-11-08 20:07 ./usr/include/gclib/gff.h
-rw-r--r-- root/root 9393 2022-11-08 20:07 ./usr/include/gclib/gsocket.h
-rw-r--r-- root/root 629 2022-11-08 20:07 ./usr/include/gclib/gstopwatch.h
-rw-r--r-- root/root 9807 2022-11-08 20:07 ./usr/include/gclib/khashl.hh
-rw-r--r-- root/root 241 2022-11-08 20:07 ./usr/include/gclib/proc_mem.h
-rw-r--r-- root/root 11838 2022-11-08 20:07 ./usr/include/gclib/wyhash.h
-rw-r--r-- root/root 184646 2022-11-08 20:07 ./usr/include/gclib/xxhash.h
drwxr-xr-x root/root 0 2022-11-08 20:07 ./usr/lib/
drwxr-xr-x root/root 0 2022-11-08 20:07 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root 541344 2022-11-08 20:07 ./usr/lib/arm-linux-gnueabihf/libgclib.a
lrwxrwxrwx root/root 0 2022-11-08 20:07 ./usr/lib/arm-linux-gnueabihf/libgclib.so -> libgclib.so.3.0.0
drwxr-xr-x root/root 0 2022-11-08 20:07 ./usr/lib/arm-linux-gnueabihf/pkgconfig/
-rw-r--r-- root/root 247 2022-11-08 20:07 ./usr/lib/arm-linux-gnueabihf/pkgconfig/libgclib.pc
drwxr-xr-x root/root 0 2022-11-08 20:07 ./usr/share/
drwxr-xr-x root/root 0 2022-11-08 20:07 ./usr/share/doc/
drwxr-xr-x root/root 0 2022-11-08 20:07 ./usr/share/doc/libgclib-dev/
-rw-r--r-- root/root 1463 2022-11-08 20:07 ./usr/share/doc/libgclib-dev/changelog.Debian.gz
-rw-r--r-- root/root 14164 2022-11-08 20:07 ./usr/share/doc/libgclib-dev/copyright
drwxr-xr-x root/root 0 2022-11-08 20:07 ./usr/share/doc/libgclib-dev/examples/
-rw-r--r-- root/root 1372 2021-07-06 01:19 ./usr/share/doc/libgclib-dev/examples/mdtest.cpp
libgclib3-dbgsym_0.12.7+ds-5_armhf.deb
--------------------------------------
new Debian package, version 2.0.
size 586124 bytes: control archive=556 bytes.
402 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: libgclib3-dbgsym
Source: libgclib
Version: 0.12.7+ds-5
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 694
Depends: libgclib3 (= 0.12.7+ds-5)
Section: debug
Priority: optional
Multi-Arch: same
Description: debug symbols for libgclib3
Build-Ids: a9d105289b97462bafe44d28d75d0180654c5df0
drwxr-xr-x root/root 0 2022-11-08 20:07 ./
drwxr-xr-x root/root 0 2022-11-08 20:07 ./usr/
drwxr-xr-x root/root 0 2022-11-08 20:07 ./usr/lib/
drwxr-xr-x root/root 0 2022-11-08 20:07 ./usr/lib/debug/
drwxr-xr-x root/root 0 2022-11-08 20:07 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2022-11-08 20:07 ./usr/lib/debug/.build-id/a9/
-rw-r--r-- root/root 699820 2022-11-08 20:07 ./usr/lib/debug/.build-id/a9/d105289b97462bafe44d28d75d0180654c5df0.debug
drwxr-xr-x root/root 0 2022-11-08 20:07 ./usr/share/
drwxr-xr-x root/root 0 2022-11-08 20:07 ./usr/share/doc/
lrwxrwxrwx root/root 0 2022-11-08 20:07 ./usr/share/doc/libgclib3-dbgsym -> libgclib3
libgclib3_0.12.7+ds-5_armhf.deb
-------------------------------
new Debian package, version 2.0.
size 121560 bytes: control archive=1200 bytes.
1145 bytes, 24 lines control
226 bytes, 3 lines md5sums
36 bytes, 1 lines shlibs
68 bytes, 2 lines triggers
Package: libgclib3
Source: libgclib
Version: 0.12.7+ds-5
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 349
Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.5), libstdc++6 (>= 5)
Section: libs
Priority: optional
Multi-Arch: same
Homepage: https://github.com/gpertea/gclib
Description: C++ library to handle biological short sequence data
This is an eclectic gathering of (mostly) C++ code which upstream used
for some bioinformatics projects. The main idea is to provide
lean code and efficient data structures, trying to avoid too many code
dependencies of heavy libraries while minimizing production cycles (and
this also implies a decent compile/build time -- looking at you,
bloated configure scripts and lengthy compile times of Boost code or
other heavy C++ template code..).
.
This code was gathered even before the C++ STL had been fully adopted as
a cross-platform "standard". Since STL by itself is a bit heavier for
most of the C++ needs, it is preferred to use simpler&leaner C++ classes
or templates for basic strings, containers, basic algorithms etc.
drwxr-xr-x root/root 0 2022-11-08 20:07 ./
drwxr-xr-x root/root 0 2022-11-08 20:07 ./usr/
drwxr-xr-x root/root 0 2022-11-08 20:07 ./usr/lib/
drwxr-xr-x root/root 0 2022-11-08 20:07 ./usr/lib/arm-linux-gnueabihf/
lrwxrwxrwx root/root 0 2022-11-08 20:07 ./usr/lib/arm-linux-gnueabihf/libgclib.so.3 -> libgclib.so.3.0.0
-rw-r--r-- root/root 329228 2022-11-08 20:07 ./usr/lib/arm-linux-gnueabihf/libgclib.so.3.0.0
drwxr-xr-x root/root 0 2022-11-08 20:07 ./usr/share/
drwxr-xr-x root/root 0 2022-11-08 20:07 ./usr/share/doc/
drwxr-xr-x root/root 0 2022-11-08 20:07 ./usr/share/doc/libgclib3/
-rw-r--r-- root/root 1463 2022-11-08 20:07 ./usr/share/doc/libgclib3/changelog.Debian.gz
-rw-r--r-- root/root 14164 2022-11-08 20:07 ./usr/share/doc/libgclib3/copyright
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 28016
Build-Time: 163
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 113
Job: libgclib_0.12.7+ds-5
Machine Architecture: armhf
Package: libgclib
Package-Time: 298
Source-Version: 0.12.7+ds-5
Space: 28016
Status: successful
Version: 0.12.7+ds-5
--------------------------------------------------------------------------------
Finished at 2022-11-11T06:50:22Z
Build needed 00:04:58, 28016k disk space