gffread →
0.12.7-2 →
armhf → 2021-12-05 05:37:00
sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019
+==============================================================================+
| gffread 0.12.7-2 (armhf) Sun, 05 Dec 2021 05:32:27 +0000 |
+==============================================================================+
Package: gffread
Version: 0.12.7-2
Source Version: 0.12.7-2
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bookworm-staging-armhf-sbuild-d7cc444a-88db-44ce-bb78-966d5df19754' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/gffread-LaDQfw/resolver-GhPZkh' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| 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 [12.6 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [13.5 MB]
Fetched 26.1 MB in 15s (1798 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'gffread' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/gffread.git
Please use:
git clone https://salsa.debian.org/med-team/gffread.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 415 kB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main gffread 0.12.7-2 (dsc) [2419 B]
Get:2 http://172.17.4.1/private bookworm-staging/main gffread 0.12.7-2 (tar) [404 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main gffread 0.12.7-2 (diff) [8536 B]
Fetched 415 kB in 0s (1073 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/gffread-LaDQfw/gffread-0.12.7' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/gffread-LaDQfw' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), libgclib-dev, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), libgclib-dev, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [957 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [379 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [459 B]
Fetched 1795 B in 0s (45.8 kB/s)
Reading package lists...
Reading package lists...
Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1
libfile-stripnondeterminism-perl libgclib-dev libgclib2 libicu67
libmagic-mgc libmagic1 libpipeline1 libsigsegv2 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 debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1
libfile-stripnondeterminism-perl libgclib-dev libgclib2 libicu67
libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool
libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-main-dummy
0 upgraded, 33 newly installed, 0 to remove and 0 not upgraded.
Need to get 17.7 MB of archives.
After this operation, 66.0 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [884 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-4 [135 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-7 [793 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.4-1 [31.6 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-2 [295 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-2 [119 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-2 [65.8 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.1 [823 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.2 [192 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 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 0.09-2 [10.2 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.1-1 [26.5 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.1-1 [15.6 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.186-1 [174 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 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 13.5.2 [1056 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf libgclib2 armhf 0.11.10+ds-2 [114 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf libgclib-dev armhf 0.11.10+ds-2 [81.0 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 17.7 MB in 5s (3677 kB/s)
Selecting previously unselected package bsdextrautils.
(Reading database ... 12552 files and directories currently installed.)
Preparing to unpack .../00-bsdextrautils_2.37.2-4_armhf.deb ...
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Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.5.4-1) ...
Setting up libgclib2:armhf (0.11.10+ds-2) ...
Setting up bsdextrautils (2.37.2-4) ...
update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
Setting up libicu67:armhf (67.1-7) ...
Setting up libmagic-mgc (1:5.41-2) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.5.2) ...
Setting up libmagic1:armhf (1:5.41-2) ...
Setting up gettext-base (0.21-4) ...
Setting up file (1:5.41-2) ...
Setting up libgclib-dev:armhf (0.11.10+ds-2) ...
Setting up autotools-dev (20180224.1+nmu1) ...
Setting up libsigsegv2:armhf (2.13-1) ...
Setting up autopoint (0.21-4) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libelf1:armhf (0.186-1) ...
Setting up libxml2:armhf (2.9.12+dfsg-5) ...
Setting up libfile-stripnondeterminism-perl (1.12.1-1) ...
Setting up gettext (0.21-4) ...
Setting up libtool (2.4.6-15) ...
Setting up m4 (1.4.18-5) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up autoconf (2.71-2) ...
Setting up dh-strip-nondeterminism (1.12.1-1) ...
Setting up dwz (0.14-1) ...
Setting up groff-base (1.22.4-7) ...
Setting up automake (1:1.16.5-1.1) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up dh-autoreconf (20) ...
Setting up debhelper (13.5.2) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.32-4+rpi1) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armhf (armv7l)
Toolchain package versions: binutils_2.37-7+rpi1 dpkg-dev_1.20.9+rpi1 g++-11_11.2.0-10+rpi1 gcc-11_11.2.0-10+rpi1 libc6-dev_2.32-4+rpi1 libstdc++-11-dev_11.2.0-10+rpi1 libstdc++6_11.2.0-10+rpi1 linux-libc-dev_5.14.16-1+rpi1
Package versions: adduser_3.118 apt_2.3.13 autoconf_2.71-2 automake_1:1.16.5-1.1 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12+rpi1 base-passwd_3.5.52 bash_5.1-5 binutils_2.37-7+rpi1 binutils-arm-linux-gnueabihf_2.37-7+rpi1 binutils-common_2.37-7+rpi1 bsdextrautils_2.37.2-4 bsdutils_1:2.37.2-4 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4.1 cpp_4:11.2.0-2+rpi1 cpp-11_11.2.0-10+rpi1 dash_0.5.11+git20210903+057cd650a4ed-3 debconf_1.5.79 debhelper_13.5.2 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.12.1-1 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.4-1 fakeroot_1.25.3-1.1 file_1:5.41-2 findutils_4.8.0-1 g++_4:11.2.0-2+rpi1 g++-11_11.2.0-10+rpi1 gcc_4:11.2.0-2+rpi1 gcc-11_11.2.0-10+rpi1 gcc-11-base_11.2.0-10+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_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.3.13 libarchive-zip-perl_1.68-1 libasan6_11.2.0-10+rpi1 libassuan0_2.5.5-1 libatomic1_11.2.0-10+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.6-1 libaudit1_1:3.0.6-1 libbinutils_2.37-7+rpi1 libblkid1_2.37.2-4 libbz2-1.0_1.0.8-4 libc-bin_2.32-4+rpi1 libc-dev-bin_2.32-4+rpi1 libc6_2.32-4+rpi1 libc6-dev_2.32-4+rpi1 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcc1-0_11.2.0-10+rpi1 libcom-err2_1.46.4-1 libcrypt-dev_1:4.4.26-1 libcrypt1_1:4.4.26-1 libctf-nobfd0_2.37-7+rpi1 libctf0_2.37-7+rpi1 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.261 libdebhelper-perl_13.5.2 libdpkg-perl_1.20.9+rpi1 libelf1_0.186-1 libext2fs2_1.46.4-1 libfakeroot_1.25.3-1.1 libffi8_3.4.2-3 libfile-stripnondeterminism-perl_1.12.1-1 libgcc-11-dev_11.2.0-10+rpi1 libgcc-s1_11.2.0-10+rpi1 libgclib-dev_0.11.10+ds-2 libgclib2_0.11.10+ds-2 libgcrypt20_1.9.4-3 libgdbm-compat4_1.22-1 libgdbm6_1.22-1 libgmp10_2:6.2.1+dfsg-3 libgnutls30_3.7.2-2 libgomp1_11.2.0-10+rpi1 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libhogweed6_3.7.3-1 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.24-2 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libksba8_1.6.0-2 libldap-2.4-2_2.4.59+dfsg-1 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.41-2 libmagic1_1:5.41-2 libmount1_2.37.2-4 libmpc3_1.2.1-1 libmpfr6_4.1.0-3 libncursesw6_6.3-1 libnettle8_3.7.3-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-5 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpcre2-8-0_10.39-3 libpcre3_2:8.39-13 libperl5.32_5.32.1-6 libpipeline1_1.5.4-1 libreadline8_8.1-2 libsasl2-2_2.1.27+dfsg2-2 libsasl2-modules-db_2.1.27+dfsg2-2 libseccomp2_2.5.3-2+rpi1 libselinux1_3.3-1 libsemanage-common_3.3-1 libsemanage2_3.3-1 libsepol1_3.1-1 libsepol2_3.3-1 libsigsegv2_2.13-1 libsmartcols1_2.37.2-4 libsqlite3-0_3.36.0-2 libss2_1.46.4-1 libssl1.1_1.1.1l-1 libstdc++-11-dev_11.2.0-10+rpi1 libstdc++6_11.2.0-10+rpi1 libsub-override-perl_0.09-2 libsystemd0_249.7-1+rpi1 libtasn1-6_4.18.0-4 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.3-1 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libubsan1_11.2.0-10+rpi1 libuchardet0_0.0.7-1 libudev1_249.7-1+rpi1 libunistring2_0.9.10-6 libuuid1_2.37.2-4 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-3+rpi1 linux-libc-dev_5.14.16-1+rpi1 login_1:4.8.1-2 logsave_1.46.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 mount_2.37.2-4 ncurses-base_6.3-1 ncurses-bin_6.3-1 passwd_1:4.8.1-2 patch_2.7.6-7 perl_5.32.1-6 perl-base_5.32.1-6 perl-modules-5.32_5.32.1-6 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021e-1 util-linux_2.37.2-4 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: gffread
Binary: gffread
Architecture: any
Version: 0.12.7-2
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>, Michael R. Crusoe <crusoe@debian.org>, Steffen Moeller <moeller@debian.org>
Homepage: https://ccb.jhu.edu/software/stringtie/gff.shtml
Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/gffread
Vcs-Git: https://salsa.debian.org/med-team/gffread.git
Testsuite: autopkgtest
Testsuite-Triggers: augustus-doc, bash, bedtools-test, cnvkit, dpkg-dev, emboss-data, emboss-test, gbrowse, genometools-common, gff2aplot, gff2ps, htslib-test, libbio-graphics-perl, optimir, proteinortho, python3-gffutils, python3-pybedtools, r-bioc-genomicfeatures, r-bioc-gviz, r-bioc-rhtslib, r-bioc-rtracklayer, seqan-apps, spades, trinityrnaseq-examples
Build-Depends: debhelper-compat (= 13), libgclib-dev
Package-List:
gffread deb science optional arch=any
Checksums-Sha1:
2d8d3e6e0e2fba6d9c4df6d194280f46b31072d1 403734 gffread_0.12.7.orig.tar.gz
36aa13d9ed14a8d29521aa44caf6ee41e8602c64 8536 gffread_0.12.7-2.debian.tar.xz
Checksums-Sha256:
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cf5c2f01e7954128e72c4ab4ca6f16eb26cb2df87d17ae5f154eb9ee67de3b15 8536 gffread_0.12.7-2.debian.tar.xz
Files:
e7b6121f75bf707b487af8850fe3d47c 403734 gffread_0.12.7.orig.tar.gz
203e5571c24811b9c617066585f88042 8536 gffread_0.12.7-2.debian.tar.xz
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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.MFgEL7Eb/trustedkeys.kbx': General error
gpgv: Signature made Fri Dec 3 11:06:51 2021 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 ./gffread_0.12.7-2.dsc
dpkg-source: info: extracting gffread in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking gffread_0.12.7.orig.tar.gz
dpkg-source: info: unpacking gffread_0.12.7-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying gclib.patch
dpkg-source: info: applying hardening
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INVOCATION_ID=1b2d35e96e094e0c905e1f5e00ab4580
JOURNAL_STREAM=8:29072680
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=117
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-d7cc444a-88db-44ce-bb78-966d5df19754
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c168027
XDG_SESSION_TYPE=unspecified
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage -us -uc -mRaspbian pi4 based autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package gffread
dpkg-buildpackage: info: source version 0.12.7-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
dh_auto_clean
make -j4 clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build -- 'LINKER=$(CXX)'
make -j4 "INSTALL=install --strip-program=true" LINKER=\$\(CXX\)
make[2]: Entering directory '/<<PKGBUILDDIR>>'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -std=c++11 -I. -I/usr/include/gclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-class-memaccess -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O0 -DDEBUG -D_DEBUG -DGDEBUG -c gffread.cpp -o gffread.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -std=c++11 -I. -I/usr/include/gclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-class-memaccess -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O0 -DDEBUG -D_DEBUG -DGDEBUG -c gff_utils.cpp -o gff_utils.o
In file included from gff_utils.cpp:1:
gff_utils.h:92:8: error: ‘GRangeParser’ does not name a type
92 | extern GRangeParser* fltRange;
| ^~~~~~~~~~~~
In file included from gffread.cpp:2:
gff_utils.h:92:8: error: ‘GRangeParser’ does not name a type
92 | extern GRangeParser* fltRange;
| ^~~~~~~~~~~~
gff_utils.h:94:8: error: ‘GRangeParser’ does not name a type
94 | extern GRangeParser* fltJunction;
| ^~~~~~~~~~~~
gff_utils.h:94:8: error: ‘GRangeParser’ does not name a type
94 | extern GRangeParser* fltJunction;
| ^~~~~~~~~~~~
gff_utils.h:160:8: error: ‘GStrSet’ is not a template
160 | extern GStrSet<> attrList;
| ^~~~~~~
gff_utils.h:161:8: error: ‘GStrSet’ is not a template
161 | extern GStrSet<> fltIDs;
| ^~~~~~~
gff_utils.h:160:8: error: ‘GStrSet’ is not a template
160 | extern GStrSet<> attrList;
| ^~~~~~~
gff_utils.h:161:8: error: ‘GStrSet’ is not a template
161 | extern GStrSet<> fltIDs;
| ^~~~~~~
gffread.cpp:160:26: error: ‘GStrSet’ is not a template
160 | void loadIDlist(FILE* f, GStrSet<> & idhash) {
| ^~~~~~~
gff_utils.cpp:50:1: error: ‘GRangeParser’ does not name a type
50 | GRangeParser* fltRange=NULL;
| ^~~~~~~~~~~~
gffread.cpp: In function ‘void loadSeqInfo(FILE*, GHash<SeqInfo*>&)’:
gffread.cpp:201:18: error: cannot convert ‘SeqInfo*’ to ‘SeqInfo**’
201 | si.Add(id, new SeqInfo(len,text));
| ^~~~~~~~~~~~~~~~~~~~~
| |
| SeqInfo*
In file included from /usr/include/gclib/GFastaIndex.h:11,
from /usr/include/gclib/GFaSeqGet.h:3,
from /usr/include/gclib/gff.h:9,
from gff_utils.h:3,
from gffread.cpp:2:
/usr/include/gclib/GHash.hh:203:64: note: initializing argument 2 of ‘OBJ* GHash<OBJ>::Add(const char*, OBJ*) [with OBJ = SeqInfo*]’
203 | template <class OBJ> OBJ* GHash<OBJ>::Add(const char* ky, OBJ* pdata) {
| ~~~~~^~~~~
gff_utils.cpp:52:1: error: ‘GRangeParser’ does not name a type
52 | GRangeParser* fltJunction=NULL;
| ^~~~~~~~~~~~
gffread.cpp: In function ‘void setTableFormat(GStr&)’:
gffread.cpp:218:35: error: cannot convert ‘ETableFieldType’ to ‘ETableFieldType*’
218 | specialFields.Add("chr", ctfGFF_chr);
| ^~~~~~~~~~
| |
| ETableFieldType
In file included from /usr/include/gclib/GFastaIndex.h:11,
from /usr/include/gclib/GFaSeqGet.h:3,
from /usr/include/gclib/gff.h:9,
from gff_utils.h:3,
from gffread.cpp:2:
/usr/include/gclib/GHash.hh:203:64: note: initializing argument 2 of ‘OBJ* GHash<OBJ>::Add(const char*, OBJ*) [with OBJ = ETableFieldType]’
203 | template <class OBJ> OBJ* GHash<OBJ>::Add(const char* ky, OBJ* pdata) {
| ~~~~~^~~~~
gffread.cpp:219:34: error: cannot convert ‘ETableFieldType’ to ‘ETableFieldType*’
219 | specialFields.Add("id", ctfGFF_ID);
| ^~~~~~~~~
| |
| ETableFieldType
In file included from /usr/include/gclib/GFastaIndex.h:11,
from /usr/include/gclib/GFaSeqGet.h:3,
from /usr/include/gclib/gff.h:9,
from gff_utils.h:3,
from gffread.cpp:2:
/usr/include/gclib/GHash.hh:203:64: note: initializing argument 2 of ‘OBJ* GHash<OBJ>::Add(const char*, OBJ*) [with OBJ = ETableFieldType]’
203 | template <class OBJ> OBJ* GHash<OBJ>::Add(const char* ky, OBJ* pdata) {
| ~~~~~^~~~~
gffread.cpp:220:38: error: cannot convert ‘ETableFieldType’ to ‘ETableFieldType*’
220 | specialFields.Add("geneid", ctfGFF_geneID);
| ^~~~~~~~~~~~~
| |
| ETableFieldType
In file included from /usr/include/gclib/GFastaIndex.h:11,
from /usr/include/gclib/GFaSeqGet.h:3,
from /usr/include/gclib/gff.h:9,
from gff_utils.h:3,
from gffread.cpp:2:
/usr/include/gclib/GHash.hh:203:64: note: initializing argument 2 of ‘OBJ* GHash<OBJ>::Add(const char*, OBJ*) [with OBJ = ETableFieldType]’
203 | template <class OBJ> OBJ* GHash<OBJ>::Add(const char* ky, OBJ* pdata) {
| ~~~~~^~~~~
gffread.cpp:221:40: error: cannot convert ‘ETableFieldType’ to ‘ETableFieldType*’
221 | specialFields.Add("genename", ctfGFF_geneName);
| ^~~~~~~~~~~~~~~
| |
| ETableFieldType
gff_utils.cpp:73:1: error: ‘GStrSet’ is not a template
73 | GStrSet<> fltIDs;
| ^~~~~~~
In file included from /usr/include/gclib/GFastaIndex.h:11,
from /usr/include/gclib/GFaSeqGet.h:3,
from /usr/include/gclib/gff.h:9,
from gff_utils.h:3,
from gffread.cpp:2:
/usr/include/gclib/GHash.hh:203:64: note: initializing argument 2 of ‘OBJ* GHash<OBJ>::Add(const char*, OBJ*) [with OBJ = ETableFieldType]’
203 | template <class OBJ> OBJ* GHash<OBJ>::Add(const char* ky, OBJ* pdata) {
| ~~~~~^~~~~
gffread.cpp:222:38: error: cannot convert ‘ETableFieldType’ to ‘ETableFieldType*’
222 | specialFields.Add("parent", ctfGFF_Parent);
| ^~~~~~~~~~~~~
| |
| ETableFieldType
In file included from /usr/include/gclib/GFastaIndex.h:11,
from /usr/include/gclib/GFaSeqGet.h:3,
from /usr/include/gclib/gff.h:9,
from gff_utils.h:3,
from gffread.cpp:2:
/usr/include/gclib/GHash.hh:203:64: note: initializing argument 2 of ‘OBJ* GHash<OBJ>::Add(const char*, OBJ*) [with OBJ = ETableFieldType]’
203 | template <class OBJ> OBJ* GHash<OBJ>::Add(const char* ky, OBJ* pdata) {
| ~~~~~^~~~~
gffread.cpp:223:39: error: cannot convert ‘ETableFieldType’ to ‘ETableFieldType*’
223 | specialFields.Add("feature", ctfGFF_feature);
| ^~~~~~~~~~~~~~
| |
| ETableFieldType
In file included from /usr/include/gclib/GFastaIndex.h:11,
from /usr/include/gclib/GFaSeqGet.h:3,
from /usr/include/gclib/gff.h:9,
from gff_utils.h:3,
from gffread.cpp:2:
/usr/include/gclib/GHash.hh:203:64: note: initializing argument 2 of ‘OBJ* GHash<OBJ>::Add(const char*, OBJ*) [with OBJ = ETableFieldType]’
203 | template <class OBJ> OBJ* GHash<OBJ>::Add(const char* ky, OBJ* pdata) {
| ~~~~~^~~~~
gffread.cpp:224:37: error: cannot convert ‘ETableFieldType’ to ‘ETableFieldType*’
224 | specialFields.Add("start", ctfGFF_start);
| ^~~~~~~~~~~~
| |
| ETableFieldType
In file included from /usr/include/gclib/GFastaIndex.h:11,
from /usr/include/gclib/GFaSeqGet.h:3,
from /usr/include/gclib/gff.h:9,
from gff_utils.h:3,
from gffread.cpp:2:
/usr/include/gclib/GHash.hh:203:64: note: initializing argument 2 of ‘OBJ* GHash<OBJ>::Add(const char*, OBJ*) [with OBJ = ETableFieldType]’
203 | template <class OBJ> OBJ* GHash<OBJ>::Add(const char* ky, OBJ* pdata) {
| ~~~~~^~~~~
gffread.cpp:225:35: error: cannot convert ‘ETableFieldType’ to ‘ETableFieldType*’
225 | specialFields.Add("end", ctfGFF_end);
| ^~~~~~~~~~
| |
| ETableFieldType
In file included from /usr/include/gclib/GFastaIndex.h:11,
from /usr/include/gclib/GFaSeqGet.h:3,
from /usr/include/gclib/gff.h:9,
from gff_utils.h:3,
from gffread.cpp:2:
/usr/include/gclib/GHash.hh:203:64: note: initializing argument 2 of ‘OBJ* GHash<OBJ>::Add(const char*, OBJ*) [with OBJ = ETableFieldType]’
203 | template <class OBJ> OBJ* GHash<OBJ>::Add(const char* ky, OBJ* pdata) {
| ~~~~~^~~~~
gffread.cpp:226:38: error: cannot convert ‘ETableFieldType’ to ‘ETableFieldType*’
226 | specialFields.Add("strand", ctfGFF_strand);
| ^~~~~~~~~~~~~
| |
| ETableFieldType
In file included from /usr/include/gclib/GFastaIndex.h:11,
from /usr/include/gclib/GFaSeqGet.h:3,
from /usr/include/gclib/gff.h:9,
from gff_utils.h:3,
from gffread.cpp:2:
/usr/include/gclib/GHash.hh:203:64: note: initializing argument 2 of ‘OBJ* GHash<OBJ>::Add(const char*, OBJ*) [with OBJ = ETableFieldType]’
203 | template <class OBJ> OBJ* GHash<OBJ>::Add(const char* ky, OBJ* pdata) {
| ~~~~~^~~~~
gffread.cpp:227:40: error: cannot convert ‘ETableFieldType’ to ‘ETableFieldType*’
227 | specialFields.Add("numexons", ctfGFF_numexons);
| ^~~~~~~~~~~~~~~
| |
| ETableFieldType
In file included from /usr/include/gclib/GFastaIndex.h:11,
from /usr/include/gclib/GFaSeqGet.h:3,
from /usr/include/gclib/gff.h:9,
from gff_utils.h:3,
from gffread.cpp:2:
/usr/include/gclib/GHash.hh:203:64: note: initializing argument 2 of ‘OBJ* GHash<OBJ>::Add(const char*, OBJ*) [with OBJ = ETableFieldType]’
203 | template <class OBJ> OBJ* GHash<OBJ>::Add(const char* ky, OBJ* pdata) {
| ~~~~~^~~~~
gffread.cpp:228:37: error: cannot convert ‘ETableFieldType’ to ‘ETableFieldType*’
228 | specialFields.Add("exons", ctfGFF_exons);
| ^~~~~~~~~~~~
| |
| ETableFieldType
In file included from /usr/include/gclib/GFastaIndex.h:11,
from /usr/include/gclib/GFaSeqGet.h:3,
from /usr/include/gclib/gff.h:9,
from gff_utils.h:3,
from gffread.cpp:2:
/usr/include/gclib/GHash.hh:203:64: note: initializing argument 2 of ‘OBJ* GHash<OBJ>::Add(const char*, OBJ*) [with OBJ = ETableFieldType]’
203 | template <class OBJ> OBJ* GHash<OBJ>::Add(const char* ky, OBJ* pdata) {
| ~~~~~^~~~~
gffread.cpp:229:35: error: cannot convert ‘ETableFieldType’ to ‘ETableFieldType*’
229 | specialFields.Add("cds", ctfGFF_cds);
| ^~~~~~~~~~
| |
| ETableFieldType
In file included from /usr/include/gclib/GFastaIndex.h:11,
from /usr/include/gclib/GFaSeqGet.h:3,
from /usr/include/gclib/gff.h:9,
from gff_utils.h:3,
from gffread.cpp:2:
/usr/include/gclib/GHash.hh:203:64: note: initializing argument 2 of ‘OBJ* GHash<OBJ>::Add(const char*, OBJ*) [with OBJ = ETableFieldType]’
203 | template <class OBJ> OBJ* GHash<OBJ>::Add(const char* ky, OBJ* pdata) {
| ~~~~~^~~~~
gffread.cpp:230:38: error: cannot convert ‘ETableFieldType’ to ‘ETableFieldType*’
230 | specialFields.Add("covlen", ctfGFF_covlen);
| ^~~~~~~~~~~~~
| |
| ETableFieldType
In file included from /usr/include/gclib/GFastaIndex.h:11,
from /usr/include/gclib/GFaSeqGet.h:3,
from /usr/include/gclib/gff.h:9,
from gff_utils.h:3,
from gffread.cpp:2:
/usr/include/gclib/GHash.hh:203:64: note: initializing argument 2 of ‘OBJ* GHash<OBJ>::Add(const char*, OBJ*) [with OBJ = ETableFieldType]’
203 | template <class OBJ> OBJ* GHash<OBJ>::Add(const char* ky, OBJ* pdata) {
| ~~~~~^~~~~
gffread.cpp:231:38: error: cannot convert ‘ETableFieldType’ to ‘ETableFieldType*’
231 | specialFields.Add("cdslen", ctfGFF_cdslen);
| ^~~~~~~~~~~~~
| |
| ETableFieldType
In file included from /usr/include/gclib/GFastaIndex.h:11,
from /usr/include/gclib/GFaSeqGet.h:3,
from /usr/include/gclib/gff.h:9,
from gff_utils.h:3,
from gffread.cpp:2:
/usr/include/gclib/GHash.hh:203:64: note: initializing argument 2 of ‘OBJ* GHash<OBJ>::Add(const char*, OBJ*) [with OBJ = ETableFieldType]’
203 | template <class OBJ> OBJ* GHash<OBJ>::Add(const char* ky, OBJ* pdata) {
| ~~~~~^~~~~
gff_utils.cpp:75:1: error: ‘GStrSet’ is not a template
75 | GStrSet<> attrList;
| ^~~~~~~
gffread.cpp: In function ‘void loadRefTable(FILE*, GHash<RefTran*>&)’:
gffread.cpp:278:23: error: cannot convert ‘RefTran*’ to ‘RefTran**’
278 | rt.Add(orig_id, new RefTran(p));
| ^~~~~~~~~~~~~~
| |
| RefTran*
In file included from /usr/include/gclib/GFastaIndex.h:11,
from /usr/include/gclib/GFaSeqGet.h:3,
from /usr/include/gclib/gff.h:9,
from gff_utils.h:3,
from gffread.cpp:2:
/usr/include/gclib/GHash.hh:203:64: note: initializing argument 2 of ‘OBJ* GHash<OBJ>::Add(const char*, OBJ*) [with OBJ = RefTran*]’
203 | template <class OBJ> OBJ* GHash<OBJ>::Add(const char* ky, OBJ* pdata) {
| ~~~~~^~~~~
gff_utils.cpp: In function ‘char* getSeqDescr(char*)’:
gff_utils.cpp:216:28: error: cannot convert ‘SeqInfo**’ to ‘SeqInfo*’ in initialization
216 | SeqInfo* seqd=seqinfo.Find(seqid);
| ~~~~~~~~~~~~^~~~~~~
| |
| SeqInfo**
gff_utils.cpp: In member function ‘bool GffLoader::checkFilters(GffObj*)’:
gff_utils.cpp:400:40: error: cannot convert ‘RefTran**’ to ‘RefTran*’ in initialization
400 | RefTran* rt=reftbl.Find(refname.chars());
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~
| |
| RefTran**
gffread.cpp: In function ‘void shutDown()’:
gffread.cpp:392:16: error: ‘fltRange’ was not declared in this scope
392 | delete fltRange;
| ^~~~~~~~
gff_utils.cpp:405:39: error: cannot convert ‘RefTran**’ to ‘RefTran*’ in assignment
405 | rt=reftbl.Find(refname.chars());
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~
| |
| RefTran**
gffread.cpp:393:16: error: ‘fltJunction’ was not declared in this scope
393 | delete fltJunction;
| ^~~~~~~~~~~
gff_utils.cpp:435:13: error: ‘fltRange’ was not declared in this scope
435 | if (fltRange!=NULL) { //filter by gseqName
| ^~~~~~~~
gff_utils.cpp:458:25: error: ‘class GffObj’ has no member named ‘removeAttrs’; did you mean ‘removeAttr’?
458 | gffrec->removeAttrs(attrList);
| ^~~~~~~~~~~
| removeAttr
gffread.cpp: In function ‘int main(int, char**)’:
gffread.cpp:412:67: error: ‘haveStdInput’ was not declared in this scope
412 | if (args.getOpt('h') || args.getOpt("help") || ( numfiles==0 && !haveStdInput())) {
| ^~~~~~~~~~~~
gff_utils.cpp:469:21: error: ‘fltJunction’ was not declared in this scope
469 | if (fltJunction!=NULL) {
| ^~~~~~~~~~~
gffread.cpp:561:9: error: ‘fltRange’ was not declared in this scope
561 | fltRange=new GRangeParser(sz);
| ^~~~~~~~
gffread.cpp:561:22: error: expected type-specifier before ‘GRangeParser’
561 | fltRange=new GRangeParser(sz);
| ^~~~~~~~~~~~
gff_utils.cpp: In member function ‘bool GffLoader::process_transcript(GFastaDb&, GffObj&)’:
gff_utils.cpp:546:41: error: invalid conversion from ‘int’ to ‘int*’ [-fpermissive]
546 | isoCounter.Add(gname,1);
| ^
| |
| int
In file included from /usr/include/gclib/GFastaIndex.h:11,
from /usr/include/gclib/GFaSeqGet.h:3,
from /usr/include/gclib/gff.h:9,
from gff_utils.h:3,
from gff_utils.cpp:1:
/usr/include/gclib/GHash.hh:203:64: note: initializing argument 2 of ‘OBJ* GHash<OBJ>::Add(const char*, OBJ*) [with OBJ = int]’
203 | template <class OBJ> OBJ* GHash<OBJ>::Add(const char* ky, OBJ* pdata) {
| ~~~~~^~~~~
gffread.cpp:571:9: error: ‘fltJunction’ was not declared in this scope
571 | fltJunction=new GRangeParser(sz);
| ^~~~~~~~~~~
gff_utils.cpp:757:42: error: ‘class GffObj’ has no member named ‘printAttrs’
757 | gffrec.printAttrs(f_y, ";", false, decodeChars, false);
| ^~~~~~~~~~
gffread.cpp:571:25: error: expected type-specifier before ‘GRangeParser’
571 | fltJunction=new GRangeParser(sz);
| ^~~~~~~~~~~~
gff_utils.cpp:768:41: error: ‘class GffObj’ has no member named ‘printAttrs’
768 | gffrec.printAttrs(f_x, ";", false, decodeChars, false);
| ^~~~~~~~~~
gff_utils.cpp:834:32: error: ‘class GffObj’ has no member named ‘printAttrs’
834 | gffrec.printAttrs(f_w, ";", false, decodeChars, false);
| ^~~~~~~~~~
gff_utils.cpp: In member function ‘bool GffLoader::placeGf(GffObj*, GenomicSeqData*)’:
gff_utils.cpp:1145:54: error: cannot convert ‘GeneInfo**’ to ‘GeneInfo*’ in initialization
1145 | GeneInfo* ginfo=gene_ids.Find(geneid);
| ~~~~~~~~~~~~~^~~~~~~~
| |
| GeneInfo**
gff_utils.cpp:1148:54: error: cannot convert ‘GeneInfo*’ to ‘GeneInfo**’
1148 | gene_ids.Add(geneid, geneinfo);
| ^~~~~~~~
| |
| GeneInfo*
In file included from /usr/include/gclib/GFastaIndex.h:11,
from /usr/include/gclib/GFaSeqGet.h:3,
from /usr/include/gclib/gff.h:9,
from gff_utils.h:3,
from gff_utils.cpp:1:
/usr/include/gclib/GHash.hh:203:64: note: initializing argument 2 of ‘OBJ* GHash<OBJ>::Add(const char*, OBJ*) [with OBJ = GeneInfo*]’
203 | template <class OBJ> OBJ* GHash<OBJ>::Add(const char* ky, OBJ* pdata) {
| ~~~~~^~~~~
gff_utils.cpp: In function ‘void collectLocusData(GList<GenomicSeqData>&, bool)’:
gff_utils.cpp:1288:72: error: invalid conversion from ‘int’ to ‘int*’ [-fpermissive]
1288 | else gnames.Add(gname.chars(), 1);
| ^
| |
| int
In file included from /usr/include/gclib/GFastaIndex.h:11,
from /usr/include/gclib/GFaSeqGet.h:3,
from /usr/include/gclib/gff.h:9,
from gff_utils.h:3,
from gff_utils.cpp:1:
/usr/include/gclib/GHash.hh:203:64: note: initializing argument 2 of ‘OBJ* GHash<OBJ>::Add(const char*, OBJ*) [with OBJ = int]’
203 | template <class OBJ> OBJ* GHash<OBJ>::Add(const char* ky, OBJ* pdata) {
| ~~~~~^~~~~
gff_utils.cpp:1294:69: error: invalid conversion from ‘int’ to ‘int*’ [-fpermissive]
1294 | geneids.Add(geneid.chars(), 1);
| ^
| |
| int
In file included from /usr/include/gclib/GFastaIndex.h:11,
from /usr/include/gclib/GFaSeqGet.h:3,
from /usr/include/gclib/gff.h:9,
from gff_utils.h:3,
from gff_utils.cpp:1:
/usr/include/gclib/GHash.hh:203:64: note: initializing argument 2 of ‘OBJ* GHash<OBJ>::Add(const char*, OBJ*) [with OBJ = int]’
203 | template <class OBJ> OBJ* GHash<OBJ>::Add(const char* ky, OBJ* pdata) {
| ~~~~~^~~~~
gff_utils.cpp:1326:72: error: invalid conversion from ‘int’ to ‘int*’ [-fpermissive]
1326 | else gnames.Add(gname, 1);
| ^
| |
| int
In file included from /usr/include/gclib/GFastaIndex.h:11,
from /usr/include/gclib/GFaSeqGet.h:3,
from /usr/include/gclib/gff.h:9,
from gff_utils.h:3,
from gff_utils.cpp:1:
/usr/include/gclib/GHash.hh:203:64: note: initializing argument 2 of ‘OBJ* GHash<OBJ>::Add(const char*, OBJ*) [with OBJ = int]’
203 | template <class OBJ> OBJ* GHash<OBJ>::Add(const char* ky, OBJ* pdata) {
| ~~~~~^~~~~
gff_utils.cpp:1332:76: error: invalid conversion from ‘int’ to ‘int*’ [-fpermissive]
1332 | geneids.Add(geneid.chars(),1);
| ^
| |
| int
In file included from /usr/include/gclib/GFastaIndex.h:11,
from /usr/include/gclib/GFaSeqGet.h:3,
from /usr/include/gclib/gff.h:9,
from gff_utils.h:3,
from gff_utils.cpp:1:
/usr/include/gclib/GHash.hh:203:64: note: initializing argument 2 of ‘OBJ* GHash<OBJ>::Add(const char*, OBJ*) [with OBJ = int]’
203 | template <class OBJ> OBJ* GHash<OBJ>::Add(const char* ky, OBJ* pdata) {
| ~~~~~^~~~~
gff_utils.cpp:1368:56: error: ‘int GHash<OBJ>::Next(int) const [with OBJ = int]’ is protected within this context
1368 | while ((key=gnames.Next(gfreq))!=NULL) {
| ~~~~~~~~~~~^~~~~~~
In file included from /usr/include/gclib/GFastaIndex.h:11,
from /usr/include/gclib/GFaSeqGet.h:3,
from /usr/include/gclib/gff.h:9,
from gff_utils.h:3,
from gff_utils.cpp:1:
/usr/include/gclib/GHash.hh:555:26: note: declared protected here
555 | template <class OBJ> int GHash<OBJ>::Next(int pos) const {
| ^~~~~~~~~~
gff_utils.cpp:1368:56: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive]
1368 | while ((key=gnames.Next(gfreq))!=NULL) {
| ~~~~~~~~~~~^~~~~~~
| |
| int
gff_utils.cpp:1376:57: error: ‘int GHash<OBJ>::Next(int) const [with OBJ = int]’ is protected within this context
1376 | while ((key=geneids.Next(gfreq))!=NULL) {
| ~~~~~~~~~~~~^~~~~~~
In file included from /usr/include/gclib/GFastaIndex.h:11,
from /usr/include/gclib/GFaSeqGet.h:3,
from /usr/include/gclib/gff.h:9,
from gff_utils.h:3,
from gff_utils.cpp:1:
/usr/include/gclib/GHash.hh:555:26: note: declared protected here
555 | template <class OBJ> int GHash<OBJ>::Next(int pos) const {
| ^~~~~~~~~~
gff_utils.cpp:1376:57: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive]
1376 | while ((key=geneids.Next(gfreq))!=NULL) {
| ~~~~~~~~~~~~^~~~~~~
| |
| int
gff_utils.cpp: In member function ‘void GffLoader::load(GList<GenomicSeqData>&, void (*)(const char*, GfList*))’:
gff_utils.cpp:1449:15: error: ‘class GffReader’ has no member named ‘procEnsemblID’
1449 | gffr->procEnsemblID(this->ensemblProc);
| ^~~~~~~~~~~~~
make[2]: *** [Makefile:72: gffread.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: *** [Makefile:72: gff_utils.o] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j4 "INSTALL=install --strip-program=true" LINKER=\$\(CXX\) returned exit code 2
make[1]: *** [debian/rules:16: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:13: binary-arch] Error 2
dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2021-12-05T05:36:56Z
Finished
--------
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 1412
Build-Time: 7
Distribution: bookworm-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 230
Job: gffread_0.12.7-2
Machine Architecture: armhf
Package: gffread
Package-Time: 269
Source-Version: 0.12.7-2
Space: 1412
Status: attempted
Version: 0.12.7-2
--------------------------------------------------------------------------------
Finished at 2021-12-05T05:36:56Z
Build needed 00:04:29, 1412k disk space