Gentoo Websites Logo
Go to: Gentoo Home Documentation Forums Lists Bugs Planet Store Wiki Get Gentoo!
Bug 591952 - sci-chemistry/gromacs-2016 : sandbox issue (XDG_xxx_DIR related)
Summary: sci-chemistry/gromacs-2016 : sandbox issue (XDG_xxx_DIR related)
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Alexey Shvetsov
URL:
Whiteboard:
Keywords:
Depends on:
Blocks: 567192 589032
  Show dependency tree
 
Reported: 2016-08-23 19:28 UTC by Toralf Förster
Modified: 2019-02-18 11:55 UTC (History)
2 users (show)

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


Attachments
emerge-history.txt (emerge-history.txt,143.98 KB, text/plain)
2016-08-23 19:28 UTC, Toralf Förster
Details
sandbox-29214.log (sandbox-29214.log,654 bytes, text/plain)
2016-08-23 19:28 UTC, Toralf Förster
Details
sci-chemistry:gromacs-2016:20160823-184013.log.bz2 (sci-chemistry:gromacs-2016:20160823-184013.log.bz2,58.73 KB, application/x-bzip2)
2016-08-23 19:28 UTC, Toralf Förster
Details
emerge-info.txt (emerge-info.txt,15.33 KB, text/plain)
2018-06-25 19:10 UTC, Toralf Förster
Details
emerge-history.txt (emerge-history.txt,41.15 KB, text/plain)
2018-06-25 19:10 UTC, Toralf Förster
Details
etc.portage.tbz2 (etc.portage.tbz2,17.04 KB, application/x-bzip)
2018-06-25 19:10 UTC, Toralf Förster
Details
logs.tbz2 (logs.tbz2,32.88 KB, application/x-bzip)
2018-06-25 19:10 UTC, Toralf Förster
Details
sandbox-23257.log (sandbox-23257.log,128.90 KB, text/plain)
2018-06-25 19:10 UTC, Toralf Förster
Details
sci-chemistry:gromacs-2018.2:20180624-221737.log.bz2 (sci-chemistry:gromacs-2018.2:20180624-221737.log.bz2,90.82 KB, application/x-bzip)
2018-06-25 19:10 UTC, Toralf Förster
Details

Note You need to log in before you can comment on or make changes to this bug.
Description Toralf Förster gentoo-dev 2016-08-23 19:28:10 UTC
This issue is forced at the tinderbox by making:

export XDG_DESKTOP_DIR="/root/Desktop"
export XDG_DOCUMENTS_DIR="/root/Documents"
export XDG_DOWNLOAD_DIR="/root/Downloads"
export XDG_MUSIC_DIR="/root/Music"
export XDG_PICTURES_DIR="/root/Pictures"
export XDG_PUBLICSHARE_DIR="/root/Public"
export XDG_TEMPLATES_DIR="/root/Templates"
export XDG_VIDEOS_DIR="/root/Videos"
export XDG_RUNTIME_DIR="/root/run"
export XDG_CONFIG_HOME="/root/config"
export XDG_CACHE_HOME="/root/cache"
export XDG_DATA_HOME="/root/share"

pls see bug #567192 too

VERSION 1.0
FORMAT: F - Function called
FORMAT: S - Access Status
FORMAT: P - Path as passed to function
FORMAT: A - Absolute Path (not canonical)
FORMAT: R - Canonical Path
FORMAT: C - Command Line

F: mkdir
S: deny
P: /root/cache
A: /root/cache
R: /root/cache
C: /usr/bin/gs -P- -dSAFER -dCompatibilityLevel=1.4 -dEPSCrop -q -P- -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -sstdout=%stderr -sOutputFile=/var/tmp/portage/sci-chemistry/gromacs-2016/work/gromacs-2016_float/docs/manual/plots/dummies.pdf -P- -dSAFER -dCompatibilityLevel=1.4 -dEPSCrop -c .setpdfwrite -f /var/tmp/portage/sci-chemistry/gromacs-2016/work/gromacs-2016/docs/manual/plots/dummies.eps 


$ cat emerge-info.txt
  -----------------------------------------------------------------

  This is an unstable amd64 chroot image (named amd64-desktop-unstable_20160821-212524) at a hardened host acting as a tinderbox.

  -----------------------------------------------------------------
  USE flags defined in ...

  ... make.conf:
USE="  pax_kernel xtpax -cdinstall -oci8 -bindist cairo cdda cgoups dec_av2 dnssec dvd -egl fpm gcj gles gpg gudev gzip havege isag ithreads jadetex javaxml jpeg kerberos ldap midi mng -mod mpeg mpg123 mpi mta nls nscd openexr -plasma plotutils png -python qt3support rdoc sdl source sourceview spice sql sqlite -ssl system-icu system-jpeg system-libevent -system-llvm tcpd theora -thinkpad threads tls tools uml vaapi vdpau webkit xcb xinerama xinetd xmp xscreensaver ziffy"

  ... /etc/portage/package.use/*:
  mail-mta/ssmtp    ssl mta
  net-misc/wget     ssl
  app-editors/emacs   -dbus -svg -ssl -gtk -gtk3
  dev-libs/boehm-gc   threads
  dev-util/cmake      -qt4 -qt5
  gnome-base/librsvg  -tools
  media-libs/mesa     -vaapi
  net-misc/iputils -caps -filecaps
  >=dev-lang/python-2.7.12:2.7 ssl
  >=dev-lang/python-3.4.5:3.4 ssl
  >=media-libs/mesa-12.0.1 egl
  >=net-misc/curl-7.50.1 ssl

  unmasked packages in /etc/portage/package.unmask/*:
  media-video/ffmpeg
  -----------------------------------------------------------------

gcc-config -l:
 [1] x86_64-pc-linux-gnu-4.9.3
 [2] x86_64-pc-linux-gnu-5.4.0 *
Available Java Virtual Machines:
  [1]   icedtea-bin-8  system-vm
Available Python interpreters, in order of preference:
  [1]   python3.4
  [2]   python2.7 (fallback)
Available Ruby profiles:
  [1]   ruby20 (with Rubygems) *
  [2]   ruby21 (with Rubygems)
  -----------------------------------------------------------------

Portage 2.3.0 (python 3.4.5-final-0, default/linux/amd64/13.0/desktop, gcc-5.4.0, glibc-2.23-r2, 4.7.2-hardened x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-4.7.2-hardened-x86_64-Intel-R-_Core-TM-_i7-3930K_CPU_@_3.20GHz-with-gentoo-2.2
KiB Mem:    65285360 total,   1649588 free
KiB Swap:   67108860 total,  67108788 free
Timestamp of repository gentoo: Tue, 23 Aug 2016 15:45:01 +0000
sh bash 4.3_p46
ld GNU ld (Gentoo 2.26.1 p1.0) 2.26.1
app-shells/bash:          4.3_p46::gentoo
dev-java/java-config:     2.2.0-r3::gentoo
dev-lang/perl:            5.24.0-r1::gentoo
dev-lang/python:          2.7.12::gentoo, 3.4.5::gentoo
dev-util/cmake:           3.6.1::gentoo
sys-apps/baselayout:      2.2-r1::gentoo
sys-apps/openrc:          0.21.3::gentoo
sys-apps/sandbox:         2.10-r2::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69-r2::gentoo
sys-devel/automake:       1.11.6-r2::gentoo, 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15-r2::gentoo
sys-devel/binutils:       2.26.1::gentoo
sys-devel/gcc:            4.9.3::gentoo, 5.4.0::gentoo
sys-devel/gcc-config:     1.8-r1::gentoo
sys-devel/libtool:        2.4.6-r2::gentoo
sys-devel/make:           4.2.1::gentoo
sys-kernel/linux-headers: 4.7::gentoo (virtual/os-headers)
sys-libs/glibc:           2.23-r2::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: 1

local
    location: /usr/local/portage
    masters: gentoo
    priority: 2

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -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/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="-march=native -O2 -pipe"
DISTDIR="/var/tmp/distfiles"
EMERGE_DEFAULT_OPTS="--verbose --verbose-conflicts --color=n --nospinner --tree --quiet-build"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync network-sandbox parallel-fetch preserve-libs protect-owned sandbox sfperms strict test-fail-continue unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://ftp.uni-erlangen.de/pub/mirrors/gentoo rsync://mirror.netcologne.de/gentoo/ ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gor.bytemark.co.uk/gentoo/ rsync://ftp.snt.utwente.nl/gentoo"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j1"
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 a52 aac acl acpi alsa amd64 berkdb bluetooth branding bzip2 cairo cdda cdr cgoups cli consolekit cracklib crypt cups cxx dbus dec_av2 dnssec dri dts dvd dvdr emboss encode exif fam firefox flac fortran fpm gcj gdbm gif glamor gles gpg gpm gtk gudev gzip havege iconv ipv6 isag ithreads jadetex javaxml jpeg kerberos lcms ldap libnotify mad midi mmx mmxext mng modules mp3 mp4 mpeg mpg123 mpi mta multilib ncurses nls nptl nscd ogg openexr opengl openmp pam pango pax_kernel pcre pdf plotutils png policykit ppds qt3support qt4 rdoc readline sdl seccomp session source sourceview spell spice sql sqlite sse sse2 startup-notification svg system-icu system-jpeg system-libevent tcpd theora threads tiff tls tools truetype udev udisks uml unicode upower usb vaapi vdpau vorbis webkit wxwidgets x264 xattr xcb xinerama xinetd xml xmp xscreensaver xtpax xv xvid ziffy 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" CAMERAS="ptp2" 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 itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" L10N="ast be bn-IN dgo la mni th" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby20 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, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
Comment 1 Toralf Förster gentoo-dev 2016-08-23 19:28:16 UTC
Created attachment 443978 [details]
emerge-history.txt
Comment 2 Toralf Förster gentoo-dev 2016-08-23 19:28:18 UTC
Created attachment 443980 [details]
sandbox-29214.log
Comment 3 Toralf Förster gentoo-dev 2016-08-23 19:28:21 UTC
Created attachment 443982 [details]
sci-chemistry:gromacs-2016:20160823-184013.log.bz2
Comment 4 Christoph Junghans (RETIRED) gentoo-dev 2016-08-23 23:52:09 UTC
commit 7cbbf1df31c9ba400f57a3888988781f31b7ce6d
Author: Christoph Junghans <ottxor@gentoo.org>
Date:   Tue Aug 23 17:51:04 2016 -0600

    sci-chemistry/gromacs: fix sandbox issue (bug #591952)

    Package-Manager: portage-2.2.28
Comment 5 Toralf Förster gentoo-dev 2018-06-25 19:10:17 UTC
got at the unstable amd64 chroot image 17.0_libressl_20180623-161904 this : sandbox issue
Comment 6 Toralf Förster gentoo-dev 2018-06-25 19:10:22 UTC
Created attachment 537212 [details]
emerge-info.txt
Comment 7 Toralf Förster gentoo-dev 2018-06-25 19:10:25 UTC
Created attachment 537214 [details]
emerge-history.txt
Comment 8 Toralf Förster gentoo-dev 2018-06-25 19:10:28 UTC
Created attachment 537216 [details]
etc.portage.tbz2
Comment 9 Toralf Förster gentoo-dev 2018-06-25 19:10:31 UTC
Created attachment 537218 [details]
logs.tbz2
Comment 10 Toralf Förster gentoo-dev 2018-06-25 19:10:34 UTC
Created attachment 537220 [details]
sandbox-23257.log
Comment 11 Toralf Förster gentoo-dev 2018-06-25 19:10:37 UTC
Created attachment 537222 [details]
sci-chemistry:gromacs-2018.2:20180624-221737.log.bz2
Comment 12 Larry the Git Cow gentoo-dev 2019-02-18 11:55:35 UTC
The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3815b25d5f2b4606ad17095b3f8591e827f0a876

commit 3815b25d5f2b4606ad17095b3f8591e827f0a876
Author:     Alexey Shvetsov <alexxy@gentoo.org>
AuthorDate: 2019-02-18 11:54:28 +0000
Commit:     Alexey Shvetsov <alexxy@gentoo.org>
CommitDate: 2019-02-18 11:55:10 +0000

    sci-chemistry/gromacs: Version bump
    
    Closes: https://bugs.gentoo.org/673350
    Closes: https://bugs.gentoo.org/673340
    Closes: https://bugs.gentoo.org/670846
    Closes: https://bugs.gentoo.org/669460
    Closes: https://bugs.gentoo.org/591952
    Package-Manager: Portage-2.3.61, Repoman-2.3.12
    Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>

 sci-chemistry/gromacs/Manifest              |   2 +
 sci-chemistry/gromacs/gromacs-2019.1.ebuild | 307 ++++++++++++++++++++++++++++
 2 files changed, 309 insertions(+)