'emerge rasmol' fails with: ... x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -I/usr/include -Dlinux -D__amd64__ -D_POSIX_C_SOURCE=199309L -D_POSIX_SOURCE -D_XOPEN_SOURCE -D_BSD_SOURCE -D_SVID_SOURCE -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DFUNCPROTO=15 -DNARROWPROTO -pthread -I/usr/include/vte-0.0 -I/usr/include/gio-unix-2.0/ -I/usr/include/cairo -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DGTKWIN -DRASMOLDIR=\"/usr/lib64/rasmol/\" -DTHIRTYTWOBIT -D_USE_RASMOL_H_ -I/usr/include -I/usr/include/cbflib -c -o molecule.o molecule.c <builtin>: recipe for target 'rasmol.o' failed make: *** [rasmol.o] Error 1 Reproducible: Always root@lynx:/usr/local/portage/sci-biology(33)# emerge --info '=sci-chemistry/rasmol-2.7.5.2::gentoo' Portage 2.2.7 (default/linux/amd64/13.0/desktop, gcc-4.8.2, glibc-2.17, 3.12.3-gentoo x86_64) ================================================================= System Settings ================================================================= System uname: Linux-3.12.3-gentoo-x86_64-Intel-R-_Core-TM-2_Duo_CPU_T8300_@_2.40GHz-with-gentoo-2.2 KiB Mem: 3987136 total, 953288 free KiB Swap: 12582908 total, 12580360 free Timestamp of tree: Sun, 08 Dec 2013 15:30:01 +0000 ld GNU ld (GNU Binutils) 2.23.2 distcc 3.1 x86_64-pc-linux-gnu [disabled] app-shells/bash: 4.2_p45 dev-java/java-config: 2.2.0 dev-lang/python: 2.7.6, 3.3.3 dev-util/cmake: 2.8.12.1-r1 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: 1.9.6-r3, 1.10.3, 1.11.6, 1.12.6, 1.14 sys-devel/binutils: 2.23.2 sys-devel/gcc: 4.8.2 sys-devel/gcc-config: 1.8 sys-devel/libtool: 2.4.2 sys-devel/make: 4.0 sys-kernel/linux-headers: 3.12 (virtual/os-headers) sys-libs/glibc: 2.17 Repositories: gentoo x11 sunrise lordvan sage-on-gentoo science local g-cpan g-octave Installed sets: @system 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-php5.3/ext-active/ /etc/php/apache2-php5.5/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cgi-php5.5/ext-active/ /etc/php/cli-php5.3/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="-march=native -O2 -pipe" GENTOO_MIRRORS="http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror http://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/ ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo ftp://ftp.tu-clausthal.de/pub/linux/gentoo ftp://ftp.easynet.nl/mirror/gentoo/ " 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_lynx" PORTDIR_OVERLAY="/var/lib/layman/x11 /var/lib/layman/sunrise /var/lib/layman/lordvan /var/lib/layman/sage-on-gentoo /var/lib/layman/science /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 cg 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 irda ithreads jabber jadetex java java6 jbig john jpeg jpeg2k kate kdepim kdrive kerberos keymap kpathsea kvm ladspa lame lapack laptop latex lcms ldap lensfun libffi libkms libnotify libsamplerate lirc live lua lzma lzo mad mail maildir mapnik math matroska media-library mercurial mikmod mkl mmx mmxext mng mod modules mono motif mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap multilib multimedia musepack musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking 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 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 sage 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 sse4 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 xemacs xetex xext xft xine xml xmlreader xmlrpc xpm xv xvid xvmc yaml youtube zlib zvbi" ABI_X86="64" ALSA_CARDS="intel8x0" 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 lvm 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 ruby 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 ruby18" USERLAND="GNU" VIDEO_CARDS="nouveau 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 ================================================================= Package Settings ================================================================= sci-chemistry/rasmol-2.7.5.2 was built with the following: USE="(multilib)" root@lynx:/usr/local/portage/sci-biology(34)# emerge -pqv '=sci-chemistry/rasmol-2.7.5.2::gentoo' [ebuild R ] sci-chemistry/rasmol-2.7.5.2
Created attachment 364968 [details] build.log
cc1: fatal error: /usr/include/cbflib/stdc-predef.h: Permission denied This is the actual error. Why can't that file be read?
(In reply to Jeroen Roovers from comment #2) > cc1: fatal error: /usr/include/cbflib/stdc-predef.h: Permission denied > > This is the actual error. Why can't that file be read? Because this file does not exist anymore: rose@leopard:/home_leopard/rose(4)$ qlist -Iv cbflib sci-libs/cbflib-0.9.3.3 rose@leopard:/home_leopard/rose(5)$ qlist -Iv cbflib | grep stdc-predef
This error is unreproducible here. I would rather guess it is from cbflib. Could you please attach a build.log from cbflib?
or something completely unrelated. I don't have any clue here.
I can't reproduce this either. cbflib-0.9.2.4 does not have the file /usr/include/cbflib/stdc-predef.h. Could that header file be pulled in by a library other than cbflib?
(In reply to Justin Lecher from comment #4) > This error is unreproducible here. I would rather guess it is from cbflib. > Could you please attach a build.log from cbflib? I just recompiled cbflib. I will attach the build.log/
Created attachment 365997 [details] /var/tmp/portage/sci-libs/cbflib-0.9.3.3/temp/build.log
But also after recompiling cbflib, 'emerge rasmol' fails with the same error.
BTW., I was searching for stdc-predef.h in all files of the rasmol tree, and could it only find in build.log: root@lynx:/root(18)# find /var/tmp/portage/sci-chemistry/rasmol-2.7.5.2/ -type f -exec grep stdc-predef.h {} \; -print cc1: fatal error: /usr/include/cbflib/stdc-predef.h: Permission denied /var/tmp/portage/sci-chemistry/rasmol-2.7.5.2/temp/build.log Then I was searching for stdc-predef.h under /usr/include: root@lynx:/root(19)# find /usr/include/ -type f -exec grep stdc-predef.h {} \; -print #include <stdc-predef.h> /usr/include/features.h root@lynx:/root(20)# ll /usr/include/features.h -rw-r--r-- 1 root root 13141 Jun 26 13:47 /usr/include/features.h root@lynx:/root(21)# qfile -v /usr/include/features.h sys-libs/glibc-2.17 (/usr/include/features.h) The error happens here only at one system. And I can not find differences in the environment settings between this and the other systems, which should be relevant to rasmol. Any idea?
I really have no clue here
Which libtool version are you using?
@toolchain, do you have any clue what is going on here?
glibc installs both /usr/include/features.h and /usr/include/stdc-predef.h. this is to be expected. make sure the permissions on the dir /usr/include/cbflib/ aren't broken.
(In reply to Justin Lecher from comment #12) > Which libtool version are you using? rose@lynx:/home/rose(2)$ qlist -Iv libtool sys-devel/libtool-2.4.2
I cannot help here. There must be something wrong on your side.
(In reply to SpanKY from comment #14) > glibc installs both /usr/include/features.h and /usr/include/stdc-predef.h. > this is to be expected. > > make sure the permissions on the dir /usr/include/cbflib/ aren't broken. At the affected system I had: rose@lynx:/home/rose(3)$ ll -d /usr/include/cbflib drw-r--r-- 2 root root 4096 23. Dez 16:59 /usr/include/cbflib/ at an other system I have: root@impala:/root(10)# ll -d /usr/include/cbflib drwxr-xr-x 2 root root 4096 Dec 7 10:45 /usr/include/cbflib/ After adding the search permission to /usr/include/cbflib I could again emerge rasmol.
So closing this now as we will not be able to figure out how the permission changes happened. Thanks Mike for the final clue.
Now I have the next system, where /usr/include/cbflib is not searchable: root@tiger:/root(8)# ll -d /usr/include/cbflib drw-r--r-- 2 root root 4096 Dec 20 06:59 /usr/include/cbflib/ I suppose, that I did not manually remove the search permission for g and o.
bad perms on a dir in /usr/include isn't really the domain of toolchain, so i'll let the respective maintainers sort things out
I have no clue what triggers this bad permissions.
