trying to emerge sci-biology/ncbi-tools with X fails as the linker can not link to libXp Reproducible: Always Steps to Reproduce: 1. emerge -v sci-biology/ncbi-tools-2.2.26-r2 (current stable) Actual Results: build fails Expected Results: build should work, either by stabilizing, or building a different version not dependent on libXp, or by patching this one according to this forum thread it seems as x11-libs/libXp existed one day but does not anymore. USE="-X" emerge -v sci-biology/ncbi-tools works
Created attachment 597606 [details] Build Log
haschka@thebox ~/Downloads $ emerge --info Portage 2.3.76 (python 3.6.9-final-0, default/linux/amd64/17.0/no-multilib, gcc-9.2.0, glibc-2.29-r2, 4.19.82-gentoo x86_64) ================================================================= System uname: Linux-4.19.82-gentoo-x86_64-Intel-R-_Core-TM-_i7-8700_CPU_@_3.20GHz-with-gentoo-2.6 KiB Mem: 7940132 total, 909280 free KiB Swap: 5092300 total, 5092300 free Timestamp of repository gentoo: Mon, 18 Nov 2019 15:30:01 +0000 Head commit of repository gentoo: 9b34492e2e41ef62fa7f1f0807b91c4e80490e4e sh bash 4.4_p23-r1 ld GNU ld (Gentoo 2.32 p2) 2.32.0 app-shells/bash: 4.4_p23-r1::gentoo dev-lang/perl: 5.28.2-r1::gentoo dev-lang/python: 2.7.16::gentoo, 3.6.9::gentoo dev-util/cmake: 3.14.6::gentoo sys-apps/baselayout: 2.6-r1::gentoo sys-apps/openrc: 0.41.2::gentoo sys-apps/sandbox: 2.13::gentoo sys-devel/autoconf: 2.13-r1::gentoo, 2.69-r4::gentoo sys-devel/automake: 1.16.1-r1::gentoo sys-devel/binutils: 2.32-r1::gentoo sys-devel/gcc: 9.2.0-r2::gentoo sys-devel/gcc-config: 2.1::gentoo sys-devel/libtool: 2.4.6-r3::gentoo sys-devel/make: 4.2.1-r4::gentoo sys-kernel/linux-headers: 4.19::gentoo (virtual/os-headers) sys-libs/glibc: 2.29-r2::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sync-rsync-verify-metamanifest: yes sync-rsync-extra-opts: sync-rsync-verify-jobs: 1 sync-rsync-verify-max-age: 24 localebuilds location: /localebuilds masters: gentoo ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="@FREE swiss-prot freedist linux-firmware linux-fw-redistributable no-source-code STRIDE SURF vmd free-noncomm" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -march=native -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-O2 -march=native -pipe" DISTDIR="/usr/portage/distfiles" ENV_UNSET="DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN 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 -march=native -pipe" 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 parallel-fetch pid-sandbox preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -march=native -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_US.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="en de fr" MAKEOPTS="-j6" PKGDIR="/usr/portage/packages" 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="/var/tmp" USE="X acl alsa amd64 berkdb bluetooth bzip2 cli crypt cxx dbus dri fontconfig fortran freetype gdbm gif iconv ipv6 jpeg lcms libtirpc mp3 ncurses nls nptl opengl openmp pam pcre pdf png readline seccomp split-usr ssl svg tcpd threads tiff truetype unicode vaapi vorbis vpx webp x264 x265 xattr xft zlib" ABI_X86="64" ADA_TARGET="gnat_2018" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" 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="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="libinput keyboard mouse" KERNEL="linux" L10N="en de fr" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" NETBEANS_MODULES="apisupport cnd groovy gsf harness ide identity j2ee java mobility nb php profiler soa visualweb webcommon websvccommon xml" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-2" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_6" PYTHON_TARGETS="python2_7 python3_6" RUBY_TARGETS="ruby24 ruby25" USERLAND="GNU" VIDEO_CARDS="intel i965" 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
appeared recently at the tinderbox image 17.1_hardened-j3-20210611-231351
Created attachment 717075 [details] emerge-info.txt
Created attachment 717078 [details] emerge-history.txt
Created attachment 717081 [details] environment
Created attachment 717084 [details] etc.portage.tar.bz2
Created attachment 717087 [details] logs.tar.bz2
Created attachment 717090 [details] sci-biology:ncbi-tools-2.2.26-r3:20210619-112206.log
Wasn't libXp removed from xorg-x11?
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 #12) > 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. I'm sorry but we removed this package because it was unmaintained, practically untouched in the last 5-6 years. It had numerous (8) open bugs which no one bothered to fix, was still stuck on EAPI-5 and had all sorts of hackeries incorporated in the ebuild. This really needed a maintainer to stay in the tree. Besides, Gentoo was one of the last distros to still package this (https://repology.org/project/ncbi-tools/versions)
