| Summary: | [RAP] sci-biology/meme-4.11.2_p2 - keepdir fails on EPREFIX installations | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Martin Mokrejš <mmokrejs> |
| Component: | Eclasses | Assignee: | Gentoo Prefix <prefix> |
| Status: | RESOLVED FIXED | ||
| Severity: | normal | ||
| Priority: | Normal | ||
| Version: | unspecified | ||
| Hardware: | All | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
dodir fails with permission errors, this is likely due to the diropts -o root. Reopen if issue persists. commit 780364970b40d3d521f6cb86f2fdf5db763c0820 Author: David Seifert <soap@gentoo.org> Date: Mon Feb 20 20:17:25 2017 +0100 sci-biology/meme: Remove use of 'diropts' Bug: https://bugs.gentoo.org/show_bug.cgi?id=608046 |
make[3]: Nothing to be done for 'install-exec-am'. /apps/gentoo/bin/mkdir -p '/apps/gentoo/var/tmp/portage/sci-biology/meme-4.11.2_p2/image//apps/gentoo/etc/meme' /apps/gentoo/usr/bin/install -c -m 644 db_general.csv db_other_genomes.csv alphabet_utilities.js ame_icon.png ame_template.html ame_template.css ame_template.js beadstring.xsl block_diagram.css block_diagram.js centrimo_graph.js centrimo_icon.png centrimo_template.html centrimo_template.css centrimo_template.js cisml.css cisml-to-gff.xsl cisml-to-gff3.xsl cisml-to-html.xsl cisml-to-text.xsl delay_draw.js dreme_icon.png dreme_template.html dreme_template.css dreme_template.js eps_context.js fimo_icon.png fimo-to-gff3.xsl fimo-to-html.xsl fimo-to-text.xsl generate_js_wrapped_template.pl generate_xsl_icons.pl gomo-to-html.xsl hmm-text.xsl job_status.tmpl mast_icon.png mast_template.css mast_template.html mast_template.js mcast_icon.png '/apps/gentoo/var/tmp/portage/sci-biology/meme-4.11.2_p2/image//apps/gentoo/etc/meme' /apps/gentoo/usr/bin/install -c -m 644 mcast_template.css mcast_template.html mcast_template.js meme.css meme_icon.png meme_template.html meme_template.css meme_template.js memechip_icon.png meme-chip_template.html meme-chip_template.css meme-chip_template.js motif_logo.js prior1.plib prior30.plib spamo_graph.js spamo_icon.png spamo_template.html spamo_template.css spamo_template.js template.eps tomtom_icon.png tomtom_template.html tomtom_template.css tomtom_template.js utilities.js constants.js constants.xsl icons.xsl logging.conf meme.css.xsl motif_logo_template.js utilities.js.xsl '/apps/gentoo/var/tmp/portage/sci-biology/meme-4.11.2_p2/image//apps/gentoo/etc/meme' make[3]: Leaving directory '/apps/gentoo/var/tmp/portage/sci-biology/meme-4.11.2_p2/work/meme_4.11.2/etc' make[2]: Leaving directory '/apps/gentoo/var/tmp/portage/sci-biology/meme-4.11.2_p2/work/meme_4.11.2/etc' make[2]: Entering directory '/apps/gentoo/var/tmp/portage/sci-biology/meme-4.11.2_p2/work/meme_4.11.2' make[3]: Entering directory '/apps/gentoo/var/tmp/portage/sci-biology/meme-4.11.2_p2/work/meme_4.11.2' make[3]: Nothing to be done for 'install-exec-am'. /apps/gentoo/bin/mkdir -p /apps/gentoo/var/tmp/portage/sci-biology/meme-4.11.2_p2/image///apps/gentoo/var/log/meme chmod a+w /apps/gentoo/var/tmp/portage/sci-biology/meme-4.11.2_p2/image///apps/gentoo/var/log/meme make install-data-hook make[4]: Entering directory '/apps/gentoo/var/tmp/portage/sci-biology/meme-4.11.2_p2/work/meme_4.11.2' /apps/gentoo/bin/mkdir -p /apps/gentoo/var/tmp/portage/sci-biology/meme-4.11.2_p2/image///apps/gentoo/usr/db make[4]: Leaving directory '/apps/gentoo/var/tmp/portage/sci-biology/meme-4.11.2_p2/work/meme_4.11.2' make[3]: Leaving directory '/apps/gentoo/var/tmp/portage/sci-biology/meme-4.11.2_p2/work/meme_4.11.2' make[2]: Leaving directory '/apps/gentoo/var/tmp/portage/sci-biology/meme-4.11.2_p2/work/meme_4.11.2' make[1]: Leaving directory '/apps/gentoo/var/tmp/portage/sci-biology/meme-4.11.2_p2/work/meme_4.11.2' install: cannot change owner and permissions of '/apps/gentoo/var/tmp/portage/sci-biology/meme-4.11.2_p2/image/apps/gentoo///var/log/meme': Operation not permitted * ERROR: sci-biology/meme-4.11.2_p2::gentoo failed (install phase): * dodir failed * * If you need support, post the output of `emerge --info '=sci-biology/meme-4.11.2_p2::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/meme-4.11.2_p2::gentoo'`. * The complete build log is located at '/apps/gentoo/var/tmp/portage/sci-biology/meme-4.11.2_p2/temp/build.log'. * The ebuild environment file is located at '/apps/gentoo/var/tmp/portage/sci-biology/meme-4.11.2_p2/temp/environment'. * Working directory: '/apps/gentoo/var/tmp/portage/sci-biology/meme-4.11.2_p2/image/apps/gentoo/usr/bin' * S: '/apps/gentoo/var/tmp/portage/sci-biology/meme-4.11.2_p2/work/meme_4.11.2' * ERROR: sci-biology/meme-4.11.2_p2::gentoo failed (install phase): * keepdir failed * * If you need support, post the output of `emerge --info '=sci-biology/meme-4.11.2_p2::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/meme-4.11.2_p2::gentoo'`. * The complete build log is located at '/apps/gentoo/var/tmp/portage/sci-biology/meme-4.11.2_p2/temp/build.log'. * The ebuild environment file is located at '/apps/gentoo/var/tmp/portage/sci-biology/meme-4.11.2_p2/temp/environment'. * Working directory: '/apps/gentoo/var/tmp/portage/sci-biology/meme-4.11.2_p2/image/apps/gentoo/usr/bin' * S: '/apps/gentoo/var/tmp/portage/sci-biology/meme-4.11.2_p2/work/meme_4.11.2' The ebuild contains AFAIK: src_install() { default docompress -x /usr/share/doc/${PF}/examples # prefix all binaries with 'meme-', in order # to prevent collisions, bug 455010 cd "${ED%/}"/usr/bin/ || die local i for i in *; do if [[ $i != meme-* ]]; then mv {,meme-}"${i}" || die fi done diropts -m ugo+rwxt -o root keepdir /var/log/meme } $ emerge --info Portage 2.3.3 (python 2.7.12-final-0, prefix/linux-standalone/amd64, gcc-4.9.4, glibc-2.23-r3, 2.6.32-642.6.2.el6.Bull.104.x86_64 x86_64) ================================================================= System uname: Linux-2.6.32-642.6.2.el6.Bull.104.x86_64-x86_64-Intel-R-_Xeon-R-_CPU_E5-2670_0_@_2.60GHz-with-redhat-6.4-Santiago KiB Mem: 131942608 total, 86608680 free KiB Swap: 65536128 total, 65514844 free Timestamp of repository gentoo: Thu, 02 Feb 2017 09:00:01 +0000 sh bash 4.4_p11 ld GNU ld (Gentoo 2.27 p1.0) 2.27 app-shells/bash: 4.4_p11::gentoo dev-java/java-config: 2.2.0-r3::gentoo dev-lang/perl: 5.24.1_rc4::gentoo dev-lang/python: 2.7.12::gentoo, 3.4.5::gentoo dev-util/cmake: 3.7.2::gentoo dev-util/pkgconfig: 0.29.1::gentoo sys-apps/baselayout: 2.3::gentoo sys-apps/sandbox: 2.10-r3::gentoo sys-devel/autoconf: 2.69-r2::gentoo sys-devel/automake: 1.14.1-r1::gentoo, 1.15-r2::gentoo sys-devel/binutils: 2.27::gentoo sys-devel/gcc: 3.4.6-r2::gentoo, 4.1.2::gentoo, 4.2.4-r1::gentoo, 4.4.7::gentoo, 4.5.4::gentoo, 4.7.4::gentoo, 4.8.5::gentoo, 4.9.3::gentoo, 4.9.4::gentoo sys-devel/gcc-config: 1.8_p20160608::rap sys-devel/libtool: 2.4.6-r2::gentoo sys-devel/make: 4.2.1::gentoo sys-kernel/linux-headers: 4.9::gentoo (virtual/os-headers) sys-libs/glibc: 2.23-r3::gentoo Repositories: gentoo location: /apps/gentoo/usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 eclass-overrides: rap rap location: /apps/gentoo/usr/portage-stage sync-type: git sync-uri: https://anongit.gentoo.org/git/proj/android.git masters: gentoo eclass-overrides: rap haskell location: /apps/gentoo/var/lib/layman/haskell masters: gentoo priority: 50 eclass-overrides: rap science location: /apps/gentoo/var/lib/layman/science masters: gentoo priority: 50 eclass-overrides: rap ACCEPT_KEYWORDS="amd64 ~amd64 ~amd64-linux" ACCEPT_LICENSE="* -@EULA dlj-1.1 sun-bcla-java-vm Oracle-BCLA-JavaSE IBM-J1.6 skype-eula Nero-EULA-US AdobeFlash-10.3 skype-4.0.0.7-copyright AdobeFlash-11.x Intel-SDP OPERA-2014" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -O2 -pipe -march=native" 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/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-O2 -pipe -O2 -pipe -march=native" DISTDIR="/apps/gentoo/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles force-prefix merge-sync news nostrip parallel-fetch preserve-libs protect-owned sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans unprivileged" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j8" PKGDIR="/apps/gentoo/usr/portage/packages" PORTAGE_CONFIGROOT="/apps/gentoo/" 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="/apps/gentoo/var/tmp" USE="X alsa amd64 apache apache2 avx avx2 berkdb boost bzip2 cairo cgi cli coin cracklib crypt cryptlib cxx dbus device-mapper dhcp dri emboss encode fax fbcon ffmpeg fontconfig fortran gbm gd gdbm gimp glpk gnutls gtk hal hwdb iconv imaging innodb ithreads java javafx javascript jce jpeg jpg js jscript keymap ladspa lapack lcms libnotify lm_sensors mad mmx modules mpi mpich2 mysql ncurses nfs nls nptl nptlonly nscd objc openmp openssl pcre pdf perl php png policykit polkit ppds pppd prefix python qt3support readline resolvconf seccomp server session slideshow sndfile sqlite sse sse2 sse3 sse4_1 sse4_2 ssl ssse3 suexec svg syslog tcl tcpd threads tiff tk truetype unicode usb v4l v4l2 vim-syntax vnc wavpack wifi x11 xcb xml xorg xrandr xv xvid xvmc zlib" ABI_X86="64" 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="kexi words flow plan sheets stage tables krita karbon braindump author" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock 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" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en_US en_GB en cs" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby21" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa dummy v4l" 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, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON