Bug 336794 – sci-biology/vienna-rna-1.8.4-r1 fails to emerge

• Product: Gentoo Linux
• Status: RESOLVED DUPLICATE

[Description Juergen Rose 2010-09-11 09:25:43 UTC]

'emerge vienna-rna' fails with:
...
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4'
>>> Completed installing vienna-rna-1.8.4-r1 into /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image/

strip: x86_64-pc-linux-gnu-strip --strip-unneeded -R .comment
   usr/lib64/perl5/site_perl/5.12.2/x86_64-linux-thread-multi/auto/RNA/RNA.so
   usr/bin/RNAfold
   usr/bin/RNAeval
   usr/bin/RNAheat
   usr/bin/RNApdist
   usr/bin/RNAdistance
   usr/bin/RNAinverse
   usr/bin/RNAplot
   usr/bin/RNAsubopt
   usr/bin/RNALfold
   usr/bin/RNAcofold
   usr/bin/RNApaln
   usr/bin/RNAduplex
   usr/bin/RNAalifold
   usr/bin/RNAplfold
   usr/bin/RNAup
   usr/bin/RNAaliduplex
   usr/bin/b2ct
   usr/bin/popt
   usr/bin/AnalyseDists
   usr/bin/AnalyseSeqs
   usr/bin/RNAforester
   usr/bin/Kinfold
   usr/bin/readseq-vienna
   usr/lib64/libRNA.a
   usr/lib64/libg2.a
ecompressdir: bzip2 -9 /usr/share/man
ecompressdir: bzip2 -9 /usr/share/info

 * QA Notice: Package has poor programming practices which may compile
 *            fine but exhibit random runtime failures.
 * AS_main.c:229: warning: attempt to free a non-heap object ‘ss’

 * 
 * QA Notice: Package has poor programming practices which may compile
 *            fine but exhibit random runtime failures.
 * 
 * /usr/include/bits/stdio2.h:34: warning: call to __builtin___sprintf_chk will always overflow destination buffer
 * /usr/include/bits/string3.h:107: warning: call to __builtin___strcpy_chk will always overflow destination buffer
 * 
 *  Please file a bug about this at http://bugs.gentoo.org/


Reproducible: Always




root@condor:/root(12)# emerge --info =sci-biology/vienna-rna-1.8.4-r1
Portage 2.1.9.3 (default/linux/amd64/10.0/desktop, gcc-4.4.4, glibc-2.12.1-r1, 2.6.35-gentoo-r5 x86_64)
=================================================================
                        System Settings
=================================================================
System uname: Linux-2.6.35-gentoo-r5-x86_64-Intel-R-_Core-TM-2_CPU_6600_@_2.40GHz-with-gentoo-2.0.1
Timestamp of tree: Sat, 11 Sep 2010 05:30:01 +0000
app-shells/bash:     4.1_p7
dev-java/java-config: 2.1.11
dev-lang/python:     2.6.5-r3, 3.1.2-r4
dev-util/cmake:      2.8.1-r2
sys-apps/baselayout: 2.0.1
sys-apps/openrc:     0.6.3
sys-apps/sandbox:    2.3-r1
sys-devel/autoconf:  2.13, 2.67
sys-devel/automake:  1.4_p6-r1, 1.7.9-r2, 1.8.5-r4, 1.9.6-r3, 1.10.3, 1.11.1
sys-devel/binutils:  2.20.1-r1
sys-devel/gcc:       4.4.4-r1
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   2.2.10
sys-devel/make:      3.81-r2
virtual/os-headers:  2.6.35 (sys-kernel/linux-headers)
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA PUEL dlj-1.1 skype-eula googleearth AdobeFlash-10.1 cadsoft"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=nocona -O2 -pipe -fomit-frame-pointer"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/X11/xkb /usr/share/config /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/eselect/postgresql /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/ext-active/ /etc/portage /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=nocona -O2 -pipe -fomit-frame-pointer"
DISTDIR="/usr/portage/distfiles"
FEATURES="assume-digests distlocks fixlafiles fixpackages news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS="-march=nocona -O2 -pipe -fomit-frame-pointer"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_US.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LINGUAS="de fr"
MAKEOPTS="-j1"
PKGDIR="/usr/portage/packages/"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/var/lib/layman/dotnet /var/lib/layman/java-overlay /var/lib/layman/lordvan /var/lib/layman/science /var/lib/layman/x11 /var/lib/layman/sunrise /var/lib/layman/arcon /usr/local/portage /var/lib/cpan"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="64bit R X Xaw3d a52 aac abiword acl acpi admin afs alsa amd64 ao apache2 applet archive arpack asf aspell assistant audacious audiofile automap automount bash-completion beagle berkdb blas blast bluetooth boo boost branding bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cg cgi chm cli consolekit corba cracklib crypt css cuda cups curl cxx daap db dbase dbi dbm dbus designer devhelp device-mapper dga dia djvu doc dri ds2490 ds9097 ds9097u dts dv dvb dvd dvdr dvi dynamicplugin eds elf emacs emboss empathy encode epiphany evo examples exif expat extensions extra extras fam fame ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fpx fts3 fuse galago garmin gd gdal gdbm gedit geoip geolocation geos gif gimp ginac git glade glib glitz gml gmp gmtsuppl gnokii gnome gnome-keyring gnome-print gnuplot gnutls gphoto2 gpm grammar graphics graphtft graphviz grass gs gsl gsm gstreamer gtk guile hal harness hddtemp hdf hdf5 hdri hlapi http httpd hvm iconv icq icu id3 ide imagemagick imap innodb inotify ipod ipv6 irda ithreads jabber jadetex java java5 java6 jbig john jpeg jpeg2k kdrive kerberos kpathsea kqemu kvm ladspa lame lapack latex latex3 lcms ldap lensfun libffi libgda libnotify libsamplerate lirc lm_sensors lua lzo mad mail maildir mailwrapper mapnik math matroska mikmod mkl mmx mmxext mng modules mono moonlight motif mozdevelop mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap multilib musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking networkmanager nfs nls nntp nptl nptlonly nsplugin ntfs ntp numarray numeric nvidia obex objc ocaml octave odbc ogdi ogg ole openexr opengl openmp overview pae pam pango pcre pda pdf perl plotutils plugins png podcast policykit posix postgres postscript ppds pppd preview-latex proj projectx pstricks pulseaudio pymol python python-bindings qemu qhull qt3support qt4 quicktime readline reflection reiserfs rle romio rpc rrdcgi rrdtool samba sasl science sdl secure-delete semantic-desktop server session sip slang slp smbclient smp sms sndfile snmp soup sox speex spell sql sqlite sse sse2 ssl startup-notification stlport subtitles subversion suexec svg swig sysfs szip t1lib tcl tcpd tex tex4ht texmacs theora threads thunderbird tidy tiff tk tntc tools truetype udev unicode usb userlocales utempter v4l2 video virtualbox vorbis wav webdav webdav-serf webkit wmf wxwidgets x264 xattr xcb xemacs xext xine xml xmlreader xmlrpc xorg xpm xulrunner xv xvid xvmc zlib zvbi" ALSA_CARDS="intel8x0" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic auth_digest authn_anon authn_dbd authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif so speling status unique_id userdir usertrack vhost_alias" CAMERAS="canon" DVB_CARDS="tda10045 tda10046lifeview" ELIBC="glibc" INPUT_DEVICES="keyboard mouse                evdev               " KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="de fr" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler ruby websvccommon xml" QEMU_SOFTMMU_TARGETS="i386 ppc ppc64 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby18 jruby" USERLAND="GNU" VIDEO_CARDS="nv nvidia nouveau vesa" 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

=================================================================
                        Package Settings
=================================================================

sci-biology/vienna-rna-1.8.4-r1 was built with the following:
USE="(multilib)" 
LDFLAGS="-Wl,-O1"



root@condor:/root(13)# emerge -pqv =sci-biology/vienna-rna-1.8.4-r1
[ebuild   R   ] sci-biology/vienna-rna-1.8.4-r1

[Comment 1 Juergen Rose 2010-09-11 09:26:35 UTC]

Created attachment 246808 [details]
/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/temp/build.log

[Comment 2 Kacper Kowalik (Xarthisius) (RETIRED) 2010-10-15 07:23:23 UTC]

Found that bug just after I've fixed 341089, sorry for not giving you the credit in the logs.

*** This bug has been marked as a duplicate of bug 341089 ***