| Summary: | sci-biology/kallisto: version bump | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Michał Górny <mgorny> |
| Component: | Current packages | Assignee: | Gentoo Science Biology related packages <sci-biology> |
| Status: | RESOLVED FIXED | ||
| Severity: | normal | CC: | mmokrejs, sci-biology |
| Priority: | Normal | Keywords: | PullRequest |
| Version: | unspecified | ||
| Hardware: | All | ||
| OS: | Linux | ||
| See Also: | https://github.com/gentoo/gentoo/pull/20044 | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
| Attachments: | build.log | ||
|
Description
Michał Górny
2019-10-05 10:20:15 UTC
Created attachment 658954 [details]
build.log
Currently there is 0.46.1 version but like -9999 from github, the build process breaks for me.
# emerge --info Portage 3.0.4 (python 3.7.9-final-0, default/linux/amd64/17.1/no-multilib, gcc-10.2.0, glibc-2.32, 5.4.58 x86_64) ================================================================= System uname: Linux-5.4.58-x86_64-Intel-R-_Core-TM-_i7-7820HQ_CPU_@_2.90GHz-with-gentoo-2.7 KiB Mem: 32814408 total, 2121572 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Sun, 30 Aug 2020 22:00:01 +0000 Head commit of repository gentoo: b85287dd1258d76ec40e9c0224eb91c60ddbb40d sh bash 5.0_p18 ld GNU ld (Gentoo 2.34 p6) 2.34.0 app-shells/bash: 5.0_p18::gentoo dev-java/java-config: 2.3.1::gentoo dev-lang/perl: 5.30.3-r1::gentoo dev-lang/python: 2.7.18-r100::stefantalpalaru, 3.6.12::gentoo, 3.7.9::gentoo, 3.8.5::gentoo, 3.9.0_rc1::gentoo dev-util/cmake: 3.18.1::gentoo sys-apps/baselayout: 2.7::gentoo sys-apps/openrc: 0.42.1::gentoo sys-apps/sandbox: 2.20::gentoo sys-devel/autoconf: 2.13-r1::gentoo, 2.69-r5::gentoo sys-devel/automake: 1.11.6-r3::gentoo, 1.13.4-r2::gentoo, 1.14.1-r2::gentoo, 1.15.1-r2::gentoo, 1.16.2::gentoo sys-devel/binutils: 2.32-r1::gentoo, 2.33.1-r1::gentoo, 2.34-r2::gentoo sys-devel/gcc: 9.2.0-r4::gentoo, 9.3.0-r1::gentoo, 10.2.0-r1::gentoo sys-devel/gcc-config: 2.3.1::gentoo sys-devel/libtool: 2.4.6-r6::gentoo sys-devel/make: 4.3::gentoo sys-kernel/linux-headers: 5.8::gentoo (virtual/os-headers) sys-libs/glibc: 2.32::gentoo Repositories: gentoo location: /scratch/usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sync-rsync-extra-opts: sync-rsync-verify-max-age: 24 sync-rsync-verify-metamanifest: yes sync-rsync-verify-jobs: 1 x-portage location: /usr/local/portage masters: gentoo priority: 0 layman location: /var/lib/layman masters: gentoo priority: 1 haskell location: /var/lib/layman/haskell masters: gentoo priority: 50 science location: /data/mmokrejs/proj/sci masters: gentoo priority: 50 stefantalpalaru location: /var/lib/layman/stefantalpalaru masters: gentoo priority: 50 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="@FREE dlj-1.1 sun-bcla-java-vm Oracle-BCLA-JavaSE IBM-J1.6 Nero-EULA-US AdobeFlash-10.3 AdobeFlash-11.x OPERA-2014 RAR Intel-SDP intel-ucode Skype-TOS vmware linux-firmware fasta vienna-rna unafold GRL MSttfEULA hplip-plugin meme mRNAmarkup ApE ICS ipw3945 finchtv modeller gmap master-pdf-editor abyss swiss-prot Aladdin AVASYS truecrypt-3.0 pyvcf Non-profit-OSL-3.0 estscan bcca_2010 oncotator Adobe blat staden CeCILL-1.1 phrap STRIDE cctbx-2.0 bh-luxi ARIADNE unRAR all-rights-reserved trf annovar_personal_only stampy-academic BSD-BroadInstitute UPennState freedist free-noncomm blasr sun-jlfgr FLI-Jena PSTT netperf sun-jsr67 xv vim.org OSGi-Specification-2.0 colt mod_fastcgi googleearth ACE AFL churchill genscan no-source-code linux-fw-redistributable ISSL JSON MPEG-4" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=native -ftree-vectorize" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /etc/stunnel/stunnel.conf /usr/lib64/libreoffice/program/sofficerc /usr/share/easy-rsa /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.3/conf /usr/share/maven-bin-3.6/conf /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c /etc/vmware-installer" CXXFLAGS="-O2 -pipe -march=native -ftree-vectorize" DISTDIR="/usr/portage/distfiles" ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN GOPATH PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR" FCFLAGS="-O2 -pipe -march=native -ftree-vectorize" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news nostrip parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe -march=native -ftree-vectorize" GENTOO_MIRRORS="http://gentoo.wheel.sk/ http://ftp.fi.muni.cz/pub/linux/gentoo/ http://gentoo.mirror.web4u.cz/ rsync://gentoo.mirror.dkm.cz/gentoo/ ftp://gentoo.mirror.web4u.cz/" LANG="cs_CZ.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="en_US en_GB en cs" MAKEOPTS="-j5" PKGDIR="/var/cache/binpkgs" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git" PORTAGE_TMPDIR="/scratch/var/tmp/" USE="X aac acpi alsa amd64 amr apache apache2 asm avx avx2 berkdb bluetooth boost bzip2 cairo caps cdda cdr cgi cli coin cracklib crypt cryptlib cryptsetup cups dbus device-mapper dhcp directfb drm dvd dvda emboss encode eselect-ldso fax fbcon ffmpeg flac fontconfig fortran gbm gcrypt gd gdbm geoip geolocation gimp glpk gmp gnutls gpm gps gtk hal hpijs hwdb iconv id3tag imaging innodb inotify ipv6 java javafx javascript jce jpeg jpg js jscript keymap ladspa lapack laptop lcms libglvnd libnotify libtirpc lm_sensors mad mariadb matroska mmx modemmanager mp3 ncurses nfs nls nptl nptlonly nscd nss ntfsprogs objc ocr ogg opengl openmp openssl opus pam parport pbs pcre pcre16 pcsc-lite pdf perl php png policykit polkit ppds pppd python qt3support qt4 qt5 readline rendering resolvconf romio scanner sctp seccomp server session slideshow smartcard sndfile split-usr sqlite sse sse2 sse3 sse4_1 sse4_2 ssl sslv3 ssse3 startup-notification suexec svg syslog tcl tcpd threads tiff tk truetype twolame udev unicode usb v4l v4l2 vim-syntax vnc vorbis wavpack wifi x11 xattr xcb xml xorg xrandr xv xvid xvmc zlib" ABI_X86="64" ADA_TARGET="gnat_2018" ALSA_CARDS="hda-intel intel8x0 intel8x0m usb-audio" APACHE2_MODULES="alias authz_host auth_basic auth_digest cgi cgid deflate dir env filter include info mem_cache mime mime_magic negotiation remoteip setenvif status userdir vhost_alias rewrite usertrack cache file_cache disk_cache charset_lite log_config log_forensic" CALLIGRA_FEATURES="karbon sheets words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx avx2 f16c fma3 mmx mmxext pclmul popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" ELIBC="glibc" GPSD_PROTOCOLS="gpsclock navcom ntrip rtcm104v2 rtcm104v3 ublox nmea0183 nmea2000 aivdm passthrough" GRUB_PLATFORMS="efi-64 pc" INPUT_DEVICES="libinput" KERNEL="linux" L10N="en-US en-GB en cs" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" OPENMPI_RM="pbs" PHP_TARGETS="php5-4 php5-5" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_6" PYTHON_TARGETS="python2_7 python3_6 python3_7" RUBY_TARGETS="ruby25 ruby27" USERLAND="GNU" VIDEO_CARDS="vesa vmware fbdev intel i915" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account" Unset: CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS Currently there is 0.46.2 and it cotains still bundled an old version of sci-biology/htslib:
kallisto-0.46.2/ext/htslib/Makefile:PACKAGE_VERSION = 1.4.1
Somehow, the "${W}"/kallisto-0.46.2/ext/htslib/ contents break for me at src_configure() step.
/scratch/var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/ext/htslib/configure: line 4: 1.4.1: command not found
/scratch/var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/ext/htslib/configure: line 5: make3:: command not found
Can't be of help here.
Also, the ebuild should respect USE=hdf5 and pass to cmake -DHDF5 to force hdf5 support. also, some LINK variable fallbacks to static in CMakeLists.txt .
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=06fc538689feab7fb91e62f619cfdc213074e8e3 commit 06fc538689feab7fb91e62f619cfdc213074e8e3 Author: David Seifert <soap@gentoo.org> AuthorDate: 2021-05-08 14:14:57 +0000 Commit: David Seifert <soap@gentoo.org> CommitDate: 2021-05-08 14:14:57 +0000 sci-biology/kallisto: Remove old 0.43.1 Closes: https://bugs.gentoo.org/696504 Closes: https://bugs.gentoo.org/708658 Closes: https://bugs.gentoo.org/788427 Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: David Seifert <soap@gentoo.org> sci-biology/kallisto/Manifest | 1 - sci-biology/kallisto/kallisto-0.43.1.ebuild | 25 ------------------------- 2 files changed, 26 deletions(-) Additionally, it has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5c94901047b60e7e21d38dea38be43e2d5f7a816 commit 5c94901047b60e7e21d38dea38be43e2d5f7a816 Author: David Seifert <soap@gentoo.org> AuthorDate: 2021-05-08 14:14:54 +0000 Commit: David Seifert <soap@gentoo.org> CommitDate: 2021-05-08 14:14:54 +0000 sci-biology/kallisto: Bump to 0.46.2 Bug: https://bugs.gentoo.org/696504 Bug: https://bugs.gentoo.org/708658 Bug: https://bugs.gentoo.org/788427 Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: David Seifert <soap@gentoo.org> sci-biology/kallisto/Manifest | 1 + .../kallisto/files/kallisto-0.46.2-catch2.patch | 38 ++++++ .../kallisto/files/kallisto-0.46.2-cmake.patch | 149 +++++++++++++++++++++ .../kallisto/files/kallisto-0.46.2-gcc11.patch | 21 +++ .../kallisto/files/kallisto-0.46.2-htslib.patch | 52 +++++++ sci-biology/kallisto/kallisto-0.46.2.ebuild | 64 +++++++++ 6 files changed, 325 insertions(+) |