| Summary: | sci-biology/ncbi-tools-2.2.26-r2 : /.../ld: cannot find -lXp | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Toralf Förster <toralf> |
| Component: | Current packages | Assignee: | Gentoo Science Biology related packages <sci-biology> |
| Status: | RESOLVED FIXED | ||
| Severity: | normal | CC: | mmokrejs, rose, treecleaner |
| Priority: | Normal | Keywords: | PMASKED |
| Version: | unspecified | ||
| Hardware: | All | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
| Attachments: |
emerge-info.txt
emerge-history.txt environment etc.portage.tbz2 logs.tbz2 sci-biology:ncbi-tools-2.2.26-r2:20180308-061447.log build.log with sci-biology/ncbi-tools-2.2.26-r3 |
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Created attachment 522958 [details]
emerge-info.txt
Created attachment 522960 [details]
emerge-history.txt
Created attachment 522962 [details]
environment
Created attachment 522964 [details]
etc.portage.tbz2
Created attachment 522966 [details]
logs.tbz2
Created attachment 522968 [details]
sci-biology:ncbi-tools-2.2.26-r2:20180308-061447.log
I have the same issue. Is there not any patch. Almost one year after the first repport it still fails. Created attachment 721648 [details]
build.log with sci-biology/ncbi-tools-2.2.26-r3
# emerge -pqv '=sci-biology/ncbi-tools-2.2.26-r3::gentoo'
[ebuild N ] sci-biology/ncbi-tools-2.2.26-r3 USE="X -doc -static-libs"
Seems some library git dropped from xorg ? https://adelie.pkgs.org/1.0/adelie-user-aarch64/libxp-dev-1.0.3-r0.apk.html # emerge --info Portage 3.0.20 (python 3.9.6-final-0, default/linux/amd64/17.1/no-multilib, gcc-10.3.0, glibc-2.33-r1, 5.4.123 x86_64) ================================================================= System uname: Linux-5.4.123-x86_64-Intel-R-_Core-TM-_i7-7820HQ_CPU_@_2.90GHz-with-glibc2.33 KiB Mem: 32813864 total, 4179468 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Fri, 02 Jul 2021 09:00:01 +0000 Head commit of repository gentoo: d423af2c1af587b69f8caed6a0047713f76c198b sh bash 5.1_p8 ld GNU ld (Gentoo 2.34 p6) 2.34.0 app-shells/bash: 5.1_p8::gentoo dev-java/java-config: 2.3.1::gentoo dev-lang/perl: 5.30.3-r1::gentoo dev-lang/python: 2.7.18_p103::stefantalpalaru, 3.6.14::gentoo, 3.7.11::gentoo, 3.8.11::gentoo, 3.9.6::gentoo dev-lang/rust: 1.47.0-r2::gentoo dev-lang/rust-bin: 1.47.0::gentoo dev-util/cmake: 3.20.5::gentoo sys-apps/baselayout: 2.7-r3::gentoo sys-apps/openrc: 0.42.1::gentoo sys-apps/sandbox: 2.24::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, 1.16.3-r1::gentoo sys-devel/binutils: 2.32-r1::gentoo, 2.33.1-r1::gentoo, 2.34-r2::gentoo, 2.35.2::gentoo, 2.36.1-r1::gentoo sys-devel/gcc: 9.3.0-r2::gentoo, 10.3.0::gentoo, 11.1.0-r1::gentoo sys-devel/gcc-config: 2.4::gentoo sys-devel/libtool: 2.4.6-r6::gentoo sys-devel/make: 4.3::gentoo sys-kernel/linux-headers: 5.12::gentoo (virtual/os-headers) sys-libs/glibc: 2.33-r1::gentoo Repositories: gentoo location: /mnt/external/scratch/usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sync-rsync-extra-opts: sync-rsync-verify-jobs: 1 sync-rsync-verify-metamanifest: yes sync-rsync-verify-max-age: 24 science location: /data/mmokrejs/proj/sci masters: gentoo priority: 0 x-portage location: /usr/local/portage masters: gentoo priority: 1 layman location: /var/lib/layman masters: gentoo priority: 2 haskell location: /var/lib/layman/haskell 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 NPSL 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 google-chrome ACE AFL churchill genscan no-source-code linux-fw-redistributable ISSL JSON MPEG-4 Apache-2.0 BSD MIT BSD-2 FSFAP unicode Subversion OPERA-2018 ms-teams-pre TeamViewer" 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 /usr/share/maven-bin-3.8/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/php/apache2-php8.0/ext-active/ /etc/php/cgi-php8.0/ext-active/ /etc/php/cli-php8.0/ext-active/ /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="/mnt/external/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://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="/mnt/external/var/tmp/portage" USE="X aac acl 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 dri dri3 drm dvd dvda elogind 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 java javafx javascript jce jpeg jpg js jscript keymap ladspa lapack laptop lcms libglvnd libnotify libtirpc lm_sensors lz4 mad mariadb matroska mmx modemmanager mp3 ncurses nfs nls nptl nptlonly nscd nss ntfsprogs objc ocr ogg opengl openh264 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 sha 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 vaapi vim-syntax vnc vorbis wavpack wifi x11 x264 x265 xattr xcb xml xorg xrandr xv xvid xvmc zlib" ABI_X86="64" ADA_TARGET="gnat_2018" ALSA_CARDS="hdspm usb-usx2y" 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" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" OFFICE_IMPLEMENTATION="libreoffice" OPENMPI_RM="pbs" PHP_TARGETS="php5-4 php5-5" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_8" PYTHON_TARGETS="python3_7 python3_8 python3_9 pypy3" RUBY_TARGETS="ruby25 ruby27 ruby30" USERLAND="GNU" VIDEO_CARDS="vesa vmware fbdev intel i915 i965" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq proto 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, RUSTFLAGS > git dropped from xorg
... got droped from xorg
# emerge -pv x11-base/xorg-drivers x11-base/xorg-proto x11-base/xorg-server x11-base/xorg-x11 These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild R ] x11-base/xorg-drivers-1.20-r2::gentoo INPUT_DEVICES="libinput -elographics -evdev -joystick -synaptics -vmmouse -void -wacom" VIDEO_CARDS="fbdev i915 i965* intel vesa vmware -amdgpu -ast -dummy (-freedreno) (-geode) -glint -mga -nouveau -nv -nvidia (-omap) -qxl -r128 -radeon -radeonsi -siliconmotion (-tegra) (-vc4) -via -virtualbox" 0 KiB [ebuild R ] x11-base/xorg-proto-2021.4::gentoo USE="-test" 0 KiB [ebuild r U ] x11-base/xorg-server-1.20.11-r1:0/1.20.11::gentoo [1.20.10-r3:0/1.20.10::gentoo] USE="elogind udev xorg -debug -dmx -doc -ipv6 -kdrive -minimal (-selinux) -suid -systemd -test -unwind -wayland -xcsecurity -xephyr -xnest -xvfb (-libressl%)" 6 325 KiB [ebuild rR ] x11-drivers/xf86-input-libinput-1.1.0::gentoo 0 KiB [ebuild rR ] x11-drivers/xf86-video-fbdev-0.5.0-r1::gentoo 0 KiB [ebuild rR ] x11-drivers/xf86-video-intel-2.99.917_p20201215::gentoo USE="dri sna tools udev xvmc -debug -uxa" 0 KiB [ebuild rR ] x11-drivers/xf86-video-vesa-2.5.0::gentoo 0 KiB [ebuild rR ] x11-drivers/xf86-video-vmware-13.3.0::gentoo 0 KiB [ebuild R ] x11-base/xorg-x11-7.4-r3::gentoo USE="fonts" 0 KiB [ebuild rR ] x11-drivers/xf86-input-evdev-2.10.6::gentoo 0 KiB [ebuild rR ] x11-drivers/xf86-input-synaptics-1.9.1::gentoo 0 KiB [ebuild rR ] x11-drivers/xf86-input-vmmouse-13.1.0-r1::gentoo 0 KiB [ebuild rR ] x11-drivers/xf86-video-vboxvideo-1.0.0::gentoo 0 KiB Total: 13 packages (1 upgrade, 12 reinstalls), Size of downloads: 6 325 KiB https://bugs.gentoo.org/649076 LibXp has been removed over 3 years ago. This package needs to go too. *** Bug 798015 has been marked as a duplicate of this bug. *** The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=59b2be273d92b67c4c7f581657151a5e7cbb63ae commit 59b2be273d92b67c4c7f581657151a5e7cbb63ae Author: Jakov Smolić <jsmolic@gentoo.org> AuthorDate: 2021-08-30 17:17:23 +0000 Commit: Jakov Smolić <jsmolic@gentoo.org> CommitDate: 2021-08-30 17:38:50 +0000 sci-biology/ncbi-tools: Remove last-rited package Closes: https://bugs.gentoo.org/649930 Closes: https://bugs.gentoo.org/782790 Closes: https://bugs.gentoo.org/741188 Closes: https://bugs.gentoo.org/715636 Closes: https://bugs.gentoo.org/710338 Closes: https://bugs.gentoo.org/701340 Closes: https://bugs.gentoo.org/586982 Closes: https://bugs.gentoo.org/295584 Signed-off-by: Jakov Smolić <jsmolic@gentoo.org> profiles/package.mask | 6 - sci-biology/ncbi-tools/Manifest | 1 - sci-biology/ncbi-tools/files/21ncbi-r1 | 6 - .../files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch | 81 ---------- .../files/ncbi-tools-2.2.26-bfr-overflow.patch | 103 ------------- .../files/ncbi-tools-2.2.26-format-security.patch | 124 --------------- .../ncbi-tools/files/ncbi-tools-extra_vib.patch | 37 ----- sci-biology/ncbi-tools/files/ncbi-tools-lop.patch | 15 -- sci-biology/ncbi-tools/files/ncbirc | 2 - sci-biology/ncbi-tools/metadata.xml | 8 - sci-biology/ncbi-tools/ncbi-tools-2.2.26-r3.ebuild | 169 --------------------- 11 files changed, 552 deletions(-) It is still developed, see https://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/2021/Aug_18_2021/README.html , albeit in c++. However, for those of use who have issues on some hosts to get that compiled, we were happy to use an older implementation in C. Why didn't you just just go the --without-x or --disable-x way? Why dropping the whole bundle? Please restore the package. (In reply to Martin Mokrejš from comment #16) > It is still developed, see > https://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/2021/Aug_18_2021/ > README.html , albeit in c++. However, for those of use who have issues on > some hosts to get that compiled, we were happy to use an older > implementation in C. > > Why didn't you just just go the --without-x or --disable-x way? Why dropping > the whole bundle? > > Please restore the package. Nope. |
PRINTID_REPORT, sizeof (id_txt) - 50); ^~~~~~ /usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lXp collect2: error: ld returned 1 exit status make: *** [makenet.unx:1421: Psequin] Error 1 FAILURE primary make status = 0, demo = 0, threaded_demo = 0, net = 2 ------------------------------------------------------------------- This is an unstable amd64 chroot image at a tinderbox (==build bot) name: 17.0-desktop-gnome-systemd_20180304-095202 ------------------------------------------------------------------- gcc-config -l: [1] x86_64-pc-linux-gnu-7.3.0 * Available Python interpreters, in order of preference: [1] python3.5 [2] python2.7 (fallback) Available Ruby profiles: [1] ruby22 (with Rubygems) [2] ruby23 (with Rubygems) * emerge -qpv sci-biology/ncbi-tools [ebuild N ] sci-biology/ncbi-tools-2.2.26-r2 USE="X -doc -static-libs" !!! The following installed packages are masked: - media-video/qt-recordmydesktop-0.3.8-r3::gentoo (masked by: package.mask) /usr/portage/profiles/package.mask: # Michael Palimaka <kensington@gentoo.org> (07 Mar 2018) # Depends on deprecated Qt 4. Dead upstream. # Masked for removal in 30 days. Bug #649116. For more information, see the MASKED PACKAGES section in the emerge man page or refer to the Gentoo Handbook.