Created attachment 373198 [details] build.log 'emerge perl' fails with: ... written lib/Config.pod updated lib/Config.pm updated lib/Config_heavy.pl Can't locate lib/Config.pm: Permission denied at configpm line 1139. makefile:476: recipe for target 'lib/Config.pod' failed make: *** [lib/Config.pod] Error 13 make: *** Waiting for unfinished jobs.... In file included from perl.h:5080:0, from perl.c:33: perl.c: In function 'S_init_tls_and_interp': thread.h:343:18: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(2, STR_WITH_LEN("panic: pthread_key_create failed\n")); \ ^ perl.c:99:2: note: in expansion of macro 'ALLOC_THREAD_KEY' ALLOC_THREAD_KEY; ^ * ERROR: dev-lang/perl-5.18.2::gentoo failed (compile phase): * emake failed root@wildcat:/root(13)# emerge --info '=dev-lang/perl-5.18.2::gentoo' Portage 2.2.8-r1 (default/linux/amd64/13.0/desktop, gcc-4.8.2, glibc-2.18-r1, 3.13.6-gentoo x86_64) ================================================================= System Settings ================================================================= System uname: Linux-3.13.6-gentoo-x86_64-Intel-R-_Core-TM-2_Duo_CPU_T7500_@_2.20GHz-with-gentoo-2.2 KiB Mem: 3971760 total, 214924 free KiB Swap: 12582908 total, 12579664 free Timestamp of tree: Fri, 21 Mar 2014 16:00:01 +0000 ld GNU ld (GNU Binutils) 2.24 distcc 3.1 x86_64-pc-linux-gnu [disabled] app-shells/bash: 4.2_p45-r1 dev-java/java-config: 2.2.0 dev-lang/python: 2.7.6, 3.3.4 dev-util/cmake: 2.8.12.2 dev-util/pkgconfig: 0.28 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.12.4 sys-apps/sandbox: 2.6-r1 sys-devel/autoconf: 2.13, 2.69 sys-devel/automake: 1.10.3, 1.11.6, 1.12.6, 1.14.1 sys-devel/binutils: 2.24-r2 sys-devel/gcc: 4.8.2 sys-devel/gcc-config: 1.8 sys-devel/libtool: 2.4.2 sys-devel/make: 4.0-r1 sys-kernel/linux-headers: 3.13 (virtual/os-headers) sys-libs/glibc: 2.18-r1 Repositories: gentoo science sunrise lordvan dlan ago x-portage g-cpan g-octave ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA PUEL Intel-SDP dlj-1.1 skype-eula skype-4.0.0.7-copyright googleearth AdobeFlash-11.x cadsoft Oracle-BCLA-JavaSE MakeMKV-EULA NVIDIA-CUDA Nero-AAC-EULA GIMPS" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /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-php5.5/ext-active/ /etc/php/cgi-php5.5/ext-active/ /etc/php/cli-php5.5/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" CXXFLAGS="-march=native -O2 -pipe" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j3" 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" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage_wildcat" PORTDIR_OVERLAY="/var/lib/layman/science /var/lib/layman/sunrise /var/lib/layman/lordvan /var/lib/layman/dlan /var/lib/layman/ago /usr/local/portage /var/lib/cpan /var/lib/g-octave" USE="64bit R X Xaw3d a52 aac acl acpi admin afs alsa amd64 ao apache2 apng applet archive armadillo arpack asf aspell atlas audacious audiofile automap automount bash-completion berkdb blas blast bluetooth bluray boost branding bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cgi chm cli cmake consolekit cracklib crypt css cups curl cxx daap db dbi dbm dbus declarative designer devhelp device-mapper dga dia dirac djvu doc dot dri ds2490 ds9097 ds9097u dts dv dvb dvd dvdr dvi dynamicplugin eds egl elf emacs emboss emf encode epiphany evo examples exif expat extensions extra extras faac faad fam ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpm fpx fuse g3dvl garmin gcj gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp git glade glib glpk gml gmp gnome gnome-keyring gnome-print gnuplot gnutls gold gphoto2 gpm grammar graphics graphtft graphviz grass gsl gsm gstreamer gtk gtk3 gudev guile hddtemp hdf hdf5 hdri html http httpd hvm hwdb iconv icq icu id3 id3tag ide imagemagick imap inotify introspection ipod ipv6 ithreads jabber jadetex jbig john jpeg jpeg2k kate kdepim kdrive kerberos keymap kpathsea kvm ladspa lame lapack laptop latex lcms ldap lensfun libffi libkms libnotify libsamplerate live lm_sensors lua lzma lzo mad mail maildir mapnik math matroska media-library mercurial mikmod mmx mmxext mng mod modules mono motif mozilla mp3 mp4 mpeg mpi mplayer mtp multilib multimedia musepack musicbrainz mysql mysqli nautilus ncurses netcdf netpbm network networking networkmanager nfs nls nntp nptl nsplugin ntfs ntp numpy obex objc ocaml ocr octave odbc ofa ogdi ogg openexr opengl openmp openvg pam pango pcre pda pdf pdl2 perl plasma plotutils plugins png podcast policykit portaudio posix postgres postscript ppds preview-latex proj projectm projectx pstricks pulseaudio python python-bindings q16 q32 qemu qhull qt3support qt4 quicktime raw readline real reiserfs reports rhythmbox rle romio rpc rrdcgi rrdtool samba sasl schroedinger science sdk sdl secure-delete semantic-desktop server session shout sip slang slp smart smbclient smp sms sndfile snmp soap sockets sound soup sox speex spell sql sqlite sse sse2 ssl ssse3 startup-notification stlport subtitles subversion sudo suexec svg svm swig systemd szip t1lib tcl tcpd tex tex4ht texmacs tgif theora thesaurus thinkpad threads thunderbird tidy tiff tk tools truetype udev udisks unicode upower usb userlocales utempter v4l vaapi vala valgrind vdpau video virt-network virtualbox visio vorbis vpx wav webdav webdav-serf webkit wifi wmf wxwidgets x264 xa xattr xcb xetex xext xft xine xml xmlreader xmlrpc xpm xv xvid xvmc yaml youtube zlib zvbi" ABI_X86="64" ALSA_CARDS="hda-intel" APACHE2_MODULES="actions alias auth_basic auth_digest authn_anon authn_dbd authn_core authn_dbm authn_default authn_file authz_core authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgid dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info lbmethod_byrequests log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif slotmem_shm so socache_shmcb speling status unique_id unixd userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="canon fuji ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CURL_SSL="nss" DRACUT_MODULES="caps dm lvm mdraid syslog" DVB_CARDS="usb-wt220u" 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 synaptics void" KERNEL="linux" LCD_DEVICES="cfontz hd44780 mtxorb ncurses X lcd2usb lcdlinux png usblcd" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="de fr ru" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler websvccommon xml" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" QEMU_SOFTMMU_TARGETS="arm i386 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby19 ruby20" USERLAND="GNU" VIDEO_CARDS="intel displaylink" 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: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, SYNC, USE_PYTHON root@wildcat:/root(14)# emerge -pqv '=dev-lang/perl-5.18.2::gentoo' [ebuild U ] dev-lang/perl-5.18.2 [5.16.3] USE="berkdb doc gdbm ithreads -debug" !!! Multiple package instances within a single package slot have been pulled !!! into the dependency graph, resulting in a slot conflict: dev-lang/perl:0 (dev-lang/perl-5.18.2::gentoo, ebuild scheduled for merge) pulled in by =dev-lang/perl-5.18* required by (virtual/perl-parent-0.228::gentoo, installed) =dev-lang/perl-5.18.2::gentoo (and 6 more with the same problems) (dev-lang/perl-5.16.3::gentoo, installed) pulled in by dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/YAML-Syck-1.270.0::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/ImageInfo-1.360.0::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/Net-SSLeay-1.558::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/WWW-RobotRules-6.20.0::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (perl-core/Module-Pluggable-4.800.0::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/Devel-Caller-2.60.0::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/yaml-0.900.0::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/Clone-0.360.0::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/IO-HTML-1.00.0::gentoo, installed) >=dev-lang/perl-5.8.8:0/5.16= required by (media-gfx/imagemagick-6.8.8.7::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (media-libs/exiftool-9.530.0::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/MIME-Types-2.040.0::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/Lab-Measurement-3.310.0::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/App-Nopaste-0.920.0::gentoo, installed) dev-lang/perl:0/5.16= required by (sci-libs/gdal-1.10.1::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/Devel-GlobalDestruction-0.120.0::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/XML-SAX-Writer-0.540.0::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (net-analyzer/net-snmp-5.7.2.1::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/PlRPC-0.202.0-r2::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/PPI-1.215.0-r1::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/Class-ErrorHandler-0.30.0::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/Sys-SigAction-0.210.0::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/Socket6-0.250.0::gentoo, installed) =dev-lang/perl-5.16* required by (virtual/perl-digest-base-1.170.0-r1::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/MooseX-Getopt-0.560.0::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/Data-OptList-0.109.0::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/Config-IniFiles-2.830.0::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (perl-core/Term-ANSIColor-4.20.0::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/File-HomeDir-1.0.0-r1::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/text-autoformat-1.669.2-r1::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/Try-Tiny-0.190.0::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/perl-tk-804.31.0-r1::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/IO-Socket-SSL-1.967.0::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/File-MimeInfo-0.210.0::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-vcs/git-1.9.0::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (perl-core/bignum-0.320.0::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/Crypt-PasswdMD5-1.400.0::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/IO-Socket-INET6-2.720.0::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/Spreadsheet-WriteExcel-2.400.0::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/Devel-LexAlias-0.50.0::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/String-Approx-3.270.0::gentoo, installed) dev-lang/perl:0/5.16= required by (net-print/cups-filters-1.0.44::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/Params-Validate-1.80.0::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/DateTime-TimeZone-1.640.0::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/Statistics-TTest-1.1.0::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/wxperl-0.991.700::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/Statistics-Distributions-1.02::gentoo, installed) dev-lang/perl:0/5.16=[-build(-)] required by (dev-perl/DateTime-Format-Mail-0.300.100-r1::gentoo, installed) (and 4 more with the same problems)
*** Bug 505286 has been marked as a duplicate of this bug. ***
It's not related to perl or gentoo. It seems, you've got a problem somewhere in your system (broken filesystem, wrong mount options, etc).
I checked the permissions for all Config.pm (first on wildcat, where 'emerge perl' failed): root@wildcat:/root(14)# find / -xdev -name Config.pm -ls 4331201 4 -rw-r--r-- 1 root root 2207 Feb 27 04:44 /usr/lib64/parrot/6.1.0/tools/lib/Parrot/Docs/Section/Config.pm 4199766 4 -rw-r--r-- 1 root root 1159 Feb 27 04:44 /usr/lib64/parrot/6.1.0/tools/lib/Parrot/Config.pm 4465769 4 -r--r--r-- 1 root root 1107 Mar 21 18:25 /usr/lib64/perl5/vendor_perl/5.16.3/Module/Build/Config.pm 4604556 12 -r--r--r-- 1 root root 11395 Aug 24 2013 /usr/lib64/perl5/vendor_perl/5.16.3/HTTP/Config.pm 5637781 4 -r--r--r-- 1 root root 415 Jan 22 04:34 /usr/lib64/perl5/vendor_perl/5.16.3/x86_64-linux-thread-multi/Tk/Config.pm 4875610 8 -r--r--r-- 1 root root 6065 Sep 19 2013 /usr/lib64/perl5/vendor_perl/5.16.3/x86_64-linux-thread-multi/Encode/Config.pm 5516532 4 -r--r--r-- 1 root root 2833 Aug 24 2013 /usr/lib64/perl5/vendor_perl/5.16.3/x86_64-linux-thread-multi/OpenGL/Config.pm 4985417 16 -r--r--r-- 1 root root 13625 Feb 11 12:29 /usr/lib64/perl5/vendor_perl/5.16.3/x86_64-linux-thread-multi/Template/Config.pm 6433281 4 -r--r--r-- 1 root root 1349 Feb 10 21:11 /usr/lib64/perl5/vendor_perl/5.16.3/x86_64-linux-thread-multi/PDL/Config.pm 6433520 4 -r-xr-xr-x 1 root root 331 Feb 10 21:11 /usr/lib64/perl5/vendor_perl/5.16.3/x86_64-linux-thread-multi/PDL/Doc/Config.pm 4461054 40 -r--r--r-- 1 root root 39519 Aug 26 2013 /usr/lib64/perl5/vendor_perl/5.16.3/Log/Log4perl/Config.pm 4470179 12 -rw-r--r-- 1 root root 9841 Feb 11 14:48 /usr/lib64/perl5/vendor_perl/5.16.3/StreamDVD/Config.pm 6304792 12 -r-xr-xr-x 1 root root 8400 Aug 24 2013 /usr/lib64/perl5/vendor_perl/5.16.3/Bio/Tools/Run/BlastPlus/Config.pm 6304788 16 -r--r--r-- 1 root root 15763 Aug 24 2013 /usr/lib64/perl5/vendor_perl/5.16.3/Bio/Tools/Run/BEDTools/Config.pm 6433247 20 -r--r--r-- 1 root root 18643 Aug 24 2013 /usr/lib64/perl5/vendor_perl/5.16.3/Bio/Tools/Run/Bowtie/Config.pm 6304790 8 -r-xr-xr-x 1 root root 5040 Aug 24 2013 /usr/lib64/perl5/vendor_perl/5.16.3/Bio/Tools/Run/Samtools/Config.pm 6433251 8 -r-xr-xr-x 1 root root 6142 Aug 24 2013 /usr/lib64/perl5/vendor_perl/5.16.3/Bio/Tools/Run/BWA/Config.pm 6433249 12 -r-xr-xr-x 1 root root 9354 Aug 24 2013 /usr/lib64/perl5/vendor_perl/5.16.3/Bio/Tools/Run/Maq/Config.pm 6951603 8 -r--r--r-- 1 root root 6589 Feb 11 12:29 /usr/lib64/perl5/vendor_perl/5.16.3/Bio/Das/AGPServer/Config.pm 6061141 32 -r--r--r-- 1 root root 29448 Aug 24 2013 /usr/lib64/perl5/vendor_perl/5.16.3/Video/DVDRip/Config.pm 4332534 4 -r--r--r-- 1 root root 567 Nov 29 15:03 /usr/lib64/perl5/vendor_perl/5.16.3/ExtUtils/MakeMaker/Config.pm 4214734 4 -r--r--r-- 1 root root 1108 Sep 6 2013 /usr/lib64/perl5/5.16.3/Module/Build/Config.pm 7088286 8 -r--r--r-- 1 root root 6065 Sep 6 2013 /usr/lib64/perl5/5.16.3/x86_64-linux-thread-multi/Encode/Config.pm 7087994 4 -r--r--r-- 1 root root 3306 Sep 6 2013 /usr/lib64/perl5/5.16.3/x86_64-linux-thread-multi/Config.pm 4335866 8 -r--r--r-- 1 root root 5037 Sep 6 2013 /usr/lib64/perl5/5.16.3/Log/Message/Config.pm 4332473 8 -r--r--r-- 1 root root 7649 Sep 6 2013 /usr/lib64/perl5/5.16.3/Net/Config.pm 4214871 24 -r--r--r-- 1 root root 23253 Sep 6 2013 /usr/lib64/perl5/5.16.3/CPANPLUS/Config.pm 3951565 4 -r--r--r-- 1 root root 570 Sep 6 2013 /usr/lib64/perl5/5.16.3/ExtUtils/MakeMaker/Config.pm 1858754 4 -rw-r--r-- 1 root root 1766 Mar 5 2013 /usr/share/automake-1.11/Automake/Config.pm 1451480 4 -rw-r--r-- 1 root root 1713 Mar 4 2013 /usr/share/automake-1.10/Automake/Config.pm 1854029 4 -rw-r--r-- 1 root root 1951 Dec 27 23:21 /usr/share/automake-1.14/Automake/Config.pm 6955819 4 -rw-r--r-- 1 root root 1800 Jan 18 2013 /usr/share/automake-1.12/Automake/Config.pm Everybody can read these files. Then I checked the permissions on leopard (where perl-5.18.2 is installed, and 'perl-cleaner --reallyall' fails): root@leopard:/usr/src(46)# find / -mount -name Config.pm -ls 3295105 4 -rw-r--r-- 1 root root 2207 Feb 26 11:17 /usr/lib64/parrot/6.1.0/tools/lib/Parrot/Docs/Section/Config.pm 3163314 4 -rw-r--r-- 1 root root 1159 Feb 26 11:17 /usr/lib64/parrot/6.1.0/tools/lib/Parrot/Config.pm 2387198 24 -r--r--r-- 1 root root 23783 Mar 21 04:32 /usr/lib64/perl5/5.18.2/CPANPLUS/Config.pm 2387062 4 -r--r--r-- 1 root root 1107 Mar 21 04:32 /usr/lib64/perl5/5.18.2/Module/Build/Config.pm 2387690 8 -r--r--r-- 1 root root 7649 Mar 21 04:32 /usr/lib64/perl5/5.18.2/Net/Config.pm 2387714 8 -r--r--r-- 1 root root 5071 Mar 21 04:32 /usr/lib64/perl5/5.18.2/Log/Message/Config.pm 2385546 4 -r--r--r-- 1 root root 567 Mar 21 04:32 /usr/lib64/perl5/5.18.2/ExtUtils/MakeMaker/Config.pm 2386636 8 -r--r--r-- 1 root root 6065 Mar 21 04:32 /usr/lib64/perl5/5.18.2/x86_64-linux-thread-multi/Encode/Config.pm 2386592 4 -r--r--r-- 1 root root 3299 Mar 21 04:32 /usr/lib64/perl5/5.18.2/x86_64-linux-thread-multi/Config.pm 2649046 4 -r--r--r-- 1 root root 1107 Mar 12 21:57 /usr/lib64/perl5/vendor_perl/5.16.3/Module/Build/Config.pm 2781241 32 -r--r--r-- 1 root root 29448 Sep 10 2013 /usr/lib64/perl5/vendor_perl/5.16.3/Video/DVDRip/Config.pm 2652257 40 -r--r--r-- 1 root root 39519 Sep 10 2013 /usr/lib64/perl5/vendor_perl/5.16.3/Log/Log4perl/Config.pm 2632269 4 -r--r--r-- 1 root root 567 Dec 2 19:58 /usr/lib64/perl5/vendor_perl/5.16.3/ExtUtils/MakeMaker/Config.pm 2652698 12 -r--r--r-- 1 root root 11395 Sep 10 2013 /usr/lib64/perl5/vendor_perl/5.16.3/HTTP/Config.pm 3284586 4 -r--r--r-- 1 root root 1349 Jan 28 14:39 /usr/lib64/perl5/vendor_perl/5.16.3/x86_64-linux-thread-multi/PDL/Config.pm 3284825 4 -r-xr-xr-x 1 root root 331 Jan 28 14:39 /usr/lib64/perl5/vendor_perl/5.16.3/x86_64-linux-thread-multi/PDL/Doc/Config.pm 3277002 8 -r--r--r-- 1 root root 6065 Sep 18 2013 /usr/lib64/perl5/vendor_perl/5.16.3/x86_64-linux-thread-multi/Encode/Config.pm 3280592 16 -r--r--r-- 1 root root 13625 Sep 10 2013 /usr/lib64/perl5/vendor_perl/5.16.3/x86_64-linux-thread-multi/Template/Config.pm 3280371 4 -r--r--r-- 1 root root 2833 Sep 10 2013 /usr/lib64/perl5/vendor_perl/5.16.3/x86_64-linux-thread-multi/OpenGL/Config.pm 2781203 12 -rw-r--r-- 1 root root 9841 Sep 10 2013 /usr/lib64/perl5/vendor_perl/5.16.3/StreamDVD/Config.pm 2780969 8 -r--r--r-- 1 root root 6589 Sep 10 2013 /usr/lib64/perl5/vendor_perl/5.16.3/Bio/Das/AGPServer/Config.pm 2780819 12 -r-xr-xr-x 1 root root 8400 Sep 10 2013 /usr/lib64/perl5/vendor_perl/5.16.3/Bio/Tools/Run/BlastPlus/Config.pm 2780920 8 -r-xr-xr-x 1 root root 6142 Sep 10 2013 /usr/lib64/perl5/vendor_perl/5.16.3/Bio/Tools/Run/BWA/Config.pm 2780918 12 -r-xr-xr-x 1 root root 9354 Sep 10 2013 /usr/lib64/perl5/vendor_perl/5.16.3/Bio/Tools/Run/Maq/Config.pm 2780817 8 -r-xr-xr-x 1 root root 5040 Sep 10 2013 /usr/lib64/perl5/vendor_perl/5.16.3/Bio/Tools/Run/Samtools/Config.pm 2780914 20 -r--r--r-- 1 root root 18643 Sep 10 2013 /usr/lib64/perl5/vendor_perl/5.16.3/Bio/Tools/Run/Bowtie/Config.pm 2780810 16 -r--r--r-- 1 root root 15763 Sep 10 2013 /usr/lib64/perl5/vendor_perl/5.16.3/Bio/Tools/Run/BEDTools/Config.pm 3025567 4 -r--r--r-- 1 root root 384 Mar 21 04:35 /usr/lib64/perl5/vendor_perl/5.18.2/x86_64-linux-thread-multi/Tk/Config.pm 3556914 4 -rw-r--r-- 1 root root 1713 Apr 17 2012 /usr/share/automake-1.10/Automake/Config.pm 3688282 4 -rw-r--r-- 1 root root 1800 Aug 1 2013 /usr/share/automake-1.12/Automake/Config.pm 4066541 4 -rw-r--r-- 1 root root 1951 Dec 27 19:46 /usr/share/automake-1.14/Automake/Config.pm 3556973 4 -rw-r--r-- 1 root root 1766 Aug 1 2013 /usr/share/automake-1.11/Automake/Config.pm 1704607 4 -rw-r--r-- 1 root root 124 Jun 5 2012 /root/.local/share/.cpan/build/Chart-Graph-3.2-oW9Reh/t/Config.pm Again, everybody can read these files. What could I still check?
(In reply to Vladimir Smirnov from comment #2) > It's not related to perl or gentoo. It seems, you've got a problem somewhere > in your system (broken filesystem, wrong mount options, etc). I thought that maybe a broken autofs has something to do with my problems. So I tried to remerge autofs. It fails with: >>> Emerging (1 of 1) net-fs/autofs-5.0.8-r1 * autofs-5.0.8.tar.bz2 SHA256 SHA512 WHIRLPOOL size ;-) ... [ ok ] * Determining the location of the kernel source code * Found kernel source directory: * /usr/src/linux * Found kernel object directory: * /lib/modules/3.13.6-gentoo/build * Found sources for kernel version: * 3.13.6-gentoo * Checking for suitable kernel configuration options... [ ok ] >>> Unpacking source... >>> Unpacking autofs-5.0.8.tar.bz2 to /var/tmp/portage/net-fs/autofs-5.0.8-r1/work >>> Source unpacked in /var/tmp/portage/net-fs/autofs-5.0.8-r1/work >>> Preparing source in /var/tmp/portage/net-fs/autofs-5.0.8-r1/work/autofs-5.0.8 ... * Applying autofs-5.0.8-ldap-wo-sasl.patch ... [ ok ] * Running eautoreconf in '/var/tmp/portage/net-fs/autofs-5.0.8-r1/work/autofs-5.0.8' ... * Running autoconf ... [ !! ] * Failed Running autoconf ! * * Include in your bugreport the contents of: * * /var/tmp/portage/net-fs/autofs-5.0.8-r1/temp/autoconf.out * ERROR: net-fs/autofs-5.0.8-r1::gentoo failed (prepare phase): root@leopard:/root(5)# cat /var/tmp/portage/net-fs/autofs-5.0.8-r1/temp/autoconf.out ***** autoconf ***** ***** PWD: /var/tmp/portage/net-fs/autofs-5.0.8-r1/work/autofs-5.0.8 ***** autoconf Can't locate Data/Dumper.pm: Permission denied at /usr/share/autoconf/Autom4te/C4che.pm line 33. BEGIN failed--compilation aborted at /usr/share/autoconf/Autom4te/C4che.pm line 33. Compilation failed in require at /usr/bin/autom4te-2.69 line 37. BEGIN failed--compilation aborted at /usr/bin/autom4te-2.69 line 37. Also the Dumper.pm are readable for everybody: root@leopard:/root(7)# find / -mount -name Dumper.pm -ls 3294618 8 -rw-r--r-- 1 root root 5106 Feb 26 11:17 /usr/lib64/parrot/6.1.0/tools/lib/Parrot/Pmc2c/Dumper.pm 2387088 4 -r--r--r-- 1 root root 446 Mar 21 04:32 /usr/lib64/perl5/5.18.2/Module/Build/Dumper.pm 2386897 44 -r--r--r-- 1 root root 43862 Mar 21 04:32 /usr/lib64/perl5/5.18.2/x86_64-linux-thread-multi/Data/Dumper.pm 2651327 4 -r--r--r-- 1 root root 446 Mar 12 21:57 /usr/lib64/perl5/vendor_perl/5.16.3/Module/Build/Dumper.pm 3284852 20 -r--r--r-- 1 root root 17687 Jan 28 14:39 /usr/lib64/perl5/vendor_perl/5.16.3/x86_64-linux-thread-multi/PDL/IO/Dumper.pm 3280633 4 -r--r--r-- 1 root root 3598 Sep 10 2013 /usr/lib64/perl5/vendor_perl/5.16.3/x86_64-linux-thread-multi/Template/Plugin/Dumper.pm 3278309 44 -r--r--r-- 1 root root 43862 Sep 10 2013 /usr/lib64/perl5/vendor_perl/5.16.3/x86_64-linux-thread-multi/Data/Dumper.pm 3026035 20 -r--r--r-- 1 root root 17207 Mar 21 04:37 /usr/lib64/perl5/vendor_perl/5.18.2/YAML/Dumper.pm 3026450 8 -r--r--r-- 1 root root 6856 Mar 21 04:40 /usr/lib64/perl5/vendor_perl/5.18.2/PPI/Dumper.pm Could it be connected with the perl INCLUDE path? root@leopard:/root(10)# perl -e "print @INC" /root/Txt/Perl/etc/perl/usr/local/lib64/perl5/5.18.2/x86_64-linux-thread-multi/usr/local/lib64/perl5/5.18.2/usr/lib64/perl5/vendor_perl/5.18.2/x86_64-linux-thread-multi/usr/lib64/perl5/vendor_perl/5.18.2/usr/local/lib64/perl5/usr/lib64/perl5/vendor_perl/5.18.1/x86_64-linux-thread-multi/usr/lib64/perl5/vendor_perl/5.18.1/usr/lib64/perl5/vendor_perl/usr/lib64/perl5/5.18.2/x86_64-linux-thread-multi/usr/lib64/perl5/5.18.2.root@leopard:/root(11)#
Could it be that the handling of PERL5LIB has changed with perl-5.18.2? Until now I had export PERL5LIB=$HOME/Txt/Perl in .bash_profile. This is for user "root" a non existing directory, but for user "rose" it is a directory with some usefull Perl modules. And perl works for years without any problems with this settings. Now with perl-5.18.2 it looks, whether perl searches only the directory $PERL5LIB, if the variable PERL5LIB is defined. At least if I unset PERL5LIB, perl-5.18.2 finds again the installed perl modules.
I have to correct, unsetting PERL5LIB is not enough that perl-5.18.2 find all perl modules. root@condor:/root(69)# unset PERL5LIB root@condor:/root(70)# genlop -c Can't locate Date/Manip.pm in @INC (you may need to install the Date::Manip module) (@INC contains: /etc/perl /usr/local/lib64/perl5/5.18.2/x86_64-linux-thread-multi /usr/local/lib64/perl5/5.18.2 /usr/lib64/perl5/vendor_perl/5.18.2/x86_64-linux-thread-multi /usr/lib64/perl5/vendor_perl/5.18.2 /usr/local/lib64/perl5 /usr/lib64/perl5/vendor_perl /usr/lib64/perl5/5.18.2/x86_64-linux-thread-multi /usr/lib64/perl5/5.18.2 .) at /usr/bin/genlop line 28. BEGIN failed--compilation aborted at /usr/bin/genlop line 28. root@condor:/root(71)# env | grep -i perl root@condor:/root(72)# perl -e "foreach \$p (@INC) {print \"\$p\n\"}" /etc/perl /usr/local/lib64/perl5/5.18.2/x86_64-linux-thread-multi /usr/local/lib64/perl5/5.18.2 /usr/lib64/perl5/vendor_perl/5.18.2/x86_64-linux-thread-multi /usr/lib64/perl5/vendor_perl/5.18.2 /usr/local/lib64/perl5 /usr/lib64/perl5/vendor_perl /usr/lib64/perl5/5.18.2/x86_64-linux-thread-multi /usr/lib64/perl5/5.18.2 . root@condor:/root(73)# genlop -c Can't locate Date/Manip.pm in @INC (you may need to install the Date::Manip module) (@INC contains: /etc/perl /usr/local/lib64/perl5/5.18.2/x86_64-linux-thread-multi /usr/local/lib64/perl5/5.18.2 /usr/lib64/perl5/vendor_perl/5.18.2/x86_64-linux-thread-multi /usr/lib64/perl5/vendor_perl/5.18.2 /usr/local/lib64/perl5 /usr/lib64/perl5/vendor_perl /usr/lib64/perl5/5.18.2/x86_64-linux-thread-multi /usr/lib64/perl5/5.18.2 .) at /usr/bin/genlop line 28. BEGIN failed--compilation aborted at /usr/bin/genlop line 28. root@condor:/root(74)# we .bash_profile [1] 13077 But after removing the setting of PERL5LIB from .bash_profile (and rebooting, I still had some errors with a physically removed physical volume) at least 'perl-cleaner --reallyall' works.
