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Bug 649930 - sci-biology/ncbi-tools-2.2.26-r2 : /.../ld: cannot find -lXp
Summary: sci-biology/ncbi-tools-2.2.26-r2 : /.../ld: cannot find -lXp
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Biology related packages
URL:
Whiteboard:
Keywords: PMASKED
: 798015 (view as bug list)
Depends on:
Blocks:
 
Reported: 2018-03-08 18:03 UTC by Toralf Förster
Modified: 2021-09-01 08:43 UTC (History)
3 users (show)

See Also:
Package list:
Runtime testing required: ---


Attachments
emerge-info.txt (emerge-info.txt,15.79 KB, text/plain)
2018-03-08 18:03 UTC, Toralf Förster
Details
emerge-history.txt (emerge-history.txt,170.16 KB, text/plain)
2018-03-08 18:03 UTC, Toralf Förster
Details
environment (environment,88.80 KB, text/plain)
2018-03-08 18:03 UTC, Toralf Förster
Details
etc.portage.tbz2 (etc.portage.tbz2,12.23 KB, application/x-bzip)
2018-03-08 18:03 UTC, Toralf Förster
Details
logs.tbz2 (logs.tbz2,868 bytes, application/x-bzip)
2018-03-08 18:03 UTC, Toralf Förster
Details
sci-biology:ncbi-tools-2.2.26-r2:20180308-061447.log (sci-biology:ncbi-tools-2.2.26-r2:20180308-061447.log,219.92 KB, text/plain)
2018-03-08 18:03 UTC, Toralf Förster
Details
build.log with sci-biology/ncbi-tools-2.2.26-r3 (build.log,320.76 KB, text/plain)
2021-07-04 10:34 UTC, Martin Mokrejš
Details

Note You need to log in before you can comment on or make changes to this bug.
Description Toralf Förster gentoo-dev 2018-03-08 18:03:01 UTC
                 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.
Comment 1 Toralf Förster gentoo-dev 2018-03-08 18:03:04 UTC
Created attachment 522958 [details]
emerge-info.txt
Comment 2 Toralf Förster gentoo-dev 2018-03-08 18:03:07 UTC
Created attachment 522960 [details]
emerge-history.txt
Comment 3 Toralf Förster gentoo-dev 2018-03-08 18:03:11 UTC
Created attachment 522962 [details]
environment
Comment 4 Toralf Förster gentoo-dev 2018-03-08 18:03:14 UTC
Created attachment 522964 [details]
etc.portage.tbz2
Comment 5 Toralf Förster gentoo-dev 2018-03-08 18:03:17 UTC
Created attachment 522966 [details]
logs.tbz2
Comment 6 Toralf Förster gentoo-dev 2018-03-08 18:03:20 UTC
Created attachment 522968 [details]
sci-biology:ncbi-tools-2.2.26-r2:20180308-061447.log
Comment 7 Juergen Rose 2018-11-16 08:49:38 UTC
I have the same issue. Is there not any patch.
Comment 8 Juergen Rose 2019-03-15 08:09:49 UTC
Almost one year after the first repport it still fails.
Comment 9 Martin Mokrejš 2021-07-04 10:34:48 UTC
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"
Comment 10 Martin Mokrejš 2021-07-04 10:41:46 UTC
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
Comment 11 Martin Mokrejš 2021-07-04 10:42:29 UTC
> git dropped from xorg

... got droped from xorg
Comment 12 Martin Mokrejš 2021-07-04 10:46:16 UTC
# 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
Comment 13 David Seifert gentoo-dev 2021-08-01 11:32:52 UTC
https://bugs.gentoo.org/649076

LibXp has been removed over 3 years ago. This package needs to go too.
Comment 14 Sam James archtester Gentoo Infrastructure gentoo-dev Security 2021-08-19 03:00:22 UTC
*** Bug 798015 has been marked as a duplicate of this bug. ***
Comment 15 Larry the Git Cow gentoo-dev 2021-08-30 17:39:12 UTC
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(-)
Comment 16 Martin Mokrejš 2021-08-31 21:08:38 UTC
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.
Comment 17 David Seifert gentoo-dev 2021-09-01 08:43:46 UTC
(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.