Bug 396657 – [science-overlay] dev-perl/Bio-BigFile-1.06 fails to emerge due to missing jkweb.a

• Product: Gentoo Linux
• Status: UNCONFIRMED ---

[Description Juergen Rose 2012-01-01 08:57:26 UTC]

'emerge Bio-BigFile' fails with:
...
 * Applying Build.PL.patch ...                                                                                                                                              [ ok ]
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/dev-perl/Bio-BigFile-1.06/work/Bio-BigFile-1.06 ...
 * Using Module::Build
 * perl Build.PL --installdirs=vendor --libdoc= --destdir=/var/tmp/portage/dev-perl/Bio-BigFile-1.06/image/ --create_packlist=0

This module requires the compiled jkweb.a library from Jim Kent's source tree.
If you haven't already done so, please download the source from
http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build the
contents of the "kent/src/lib" subdirectory as directed in the README. Then
enter the location of the "kent/src" subdirectory at the prompt below. To prevent
this message from appearing in the future, set the environment variable KENT_SRC 
to point to the "kent/src" subdirectory.

Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'Bio-BigFile' version '1.06'
>>> Source configured.
>>> Compiling source in /var/tmp/portage/dev-perl/Bio-BigFile-1.06/work/Bio-BigFile-1.06 ...
Building Bio-BigFile
x86_64-pc-linux-gnu-gcc -I/usr/include/ucsc-genome-browser -I/usr/lib64/perl5/5.12.4/x86_64-linux-thread-multi/CORE -DXS_VERSION="1.06" -DVERSION="1.06" -fPIC -Wno-format -Wformat=0 -DMACHTYPE_ -c -march=amdfam10 -O2 -pipe -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -march=amdfam10 -O2 -pipe -o lib/Bio/DB/BigFile.o lib/Bio/DB/BigFile.c
ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
x86_64-pc-linux-gnu-gcc -shared -march=amdfam10 -O2 -pipe -Wl,-O1 -Wl,--as-needed -o blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o /jkweb.a -lz -lssl
x86_64-pc-linux-gnu-gcc: /jkweb.a: No such file or directory
error building blib/arch/auto/Bio/DB/BigFile/BigFile.so from lib/Bio/DB/BigFile.o at /usr/lib64/perl5/vendor_perl/5.12.4/ExtUtils/CBuilder/Base.pm line 310.
 * ERROR: dev-perl/Bio-BigFile-1.06 failed (compile phase):
 *   Compilation failed



I could not find any jkweb package, neither in the portage tree nor in the science overlay:

root@impala:/root(27)# eix-update;  eix jkweb
Reading Portage settings ..
Building database (/var/cache/eix) ..
[0] "gentoo" /usr/portage_impala/ (cache: metadata-flat)
     Reading category 156|156 (100%) Finished             
[1] "x11" /var/lib/layman/x11 (cache: parse|ebuild*#metadata-md5#metadata-flat#assign)
     Reading category 156|156 (100%) Finished          
[2] "lordvan" /var/lib/layman/lordvan (cache: parse|ebuild*#metadata-md5#metadata-flat#assign)
     Reading category 156|156 (100%) Finished       
[3] "bicatali" /var/lib/layman/bicatali (cache: parse|ebuild*#metadata-md5#metadata-flat#assign)
     Reading category 156|156 (100%) Finished    
[4] "science" /var/lib/layman/science (cache: parse|ebuild*#metadata-md5#metadata-flat#assign)
     Reading category 156|156 (100%) Finished             
[5] "sage-on-gentoo" /var/lib/layman/sage-on-gentoo (cache: parse|ebuild*#metadata-md5#metadata-flat#assign)
     Reading category 156|156 (100%) Finished           
[6] "java-overlay" /var/lib/layman/java-overlay (cache: parse|ebuild*#metadata-md5#metadata-flat#assign)
     Reading category 156|156 (100%) Finished           
[7] "sunrise" /var/lib/layman/sunrise (cache: parse|ebuild*#metadata-md5#metadata-flat#assign)
     Reading category 156|156 (100%) Finished             
[8] "" /usr/local/portage (cache: parse|ebuild*#metadata-md5#metadata-flat#assign)
     Reading category 117|156 ( 75%): sci-electronics .. * 
 * "/usr/local/portage/sci-electronics/libk8055/libk8055-0.2-r2.ebuild":
 * Deprecation Warning: Usage of distutils.eclass in packages not supporting installation
 * for multiple Python ABIs in EAPI <=2 is deprecated and will be banned on 2011-06-01.
 * The ebuild needs to be fixed. Please report a bug, if it has not been already reported.
 * 
     Reading category 156|156 (100%) Finished           
[9] "" /var/lib/cpan (cache: parse|ebuild*#metadata-md5#metadata-flat#assign)
     Reading category 156|156 (100%) Finished      
[10] "g-octave" /var/lib/g-octave (cache: parse|ebuild*#metadata-md5#metadata-flat#assign)
     Reading category 156|156 (100%) Finished    
Applying masks ..
Calculating hash tables ..
Writing database file /var/cache/eix ..
Database contains 16833 packages in 156 categories.
No matches found.


So I suppose a jkweb package should be added to the science overlay and a dependency should be added to Bio-BigFile.


Reproducible: Always




root@impala:/root(25)# emerge --info =dev-perl/Bio-BigFile-1.06
Portage 2.1.10.44 (default/linux/amd64/10.0, gcc-4.5.3, glibc-2.14.1-r1, 3.1.5-gentoo x86_64)
=================================================================
                        System Settings
=================================================================
System uname: Linux-3.1.5-gentoo-x86_64-AMD_Phenom-tm-_II_X4_965_Processor-with-gentoo-2.1
Timestamp of tree: Sun, 01 Jan 2012 07:30:01 +0000
app-shells/bash:          4.2_p20
dev-java/java-config:     2.1.11-r3
dev-lang/python:          2.7.2-r3::sage-on-gentoo, 3.2.2
dev-util/cmake:           2.8.6-r4
dev-util/pkgconfig:       0.26
sys-apps/baselayout:      2.1
sys-apps/openrc:          0.9.7
sys-apps/sandbox:         2.5
sys-devel/autoconf:       2.13, 2.68
sys-devel/automake:       1.9.6-r3, 1.10.3, 1.11.2
sys-devel/binutils:       2.22-r1
sys-devel/gcc:            4.5.3-r2
sys-devel/gcc-config:     1.5-r2
sys-devel/libtool:        2.4.2
sys-devel/make:           3.82-r3
sys-kernel/linux-headers: 3.1 (virtual/os-headers)
sys-libs/glibc:           2.14.1-r1
Repositories: gentoo x11 lordvan bicatali science sage-on-gentoo java-overlay sunrise x-portage x-cpan g-octave
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA PUEL dlj-1.1 skype-eula googleearth AdobeFlash-10.1 cadsoft Oracle-BCLA-JavaSE"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=amdfam10 -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.0/conf /usr/share/openvpn/easy-rsa /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.3/ext-active/ /etc/php/apache2-php5.4/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cgi-php5.4/ext-active/ /etc/php/cli-php5.3/ext-active/ /etc/php/cli-php5.4/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=amdfam10 -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="assume-digests binpkg-logs distlocks ebuild-locks fixlafiles news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS=""
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_US.UTF-8"
LC_ALL="C"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LINGUAS="de fr"
MAKEOPTS="-j5"
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/x11 /var/lib/layman/lordvan /var/lib/layman/bicatali /var/lib/layman/science /var/lib/layman/sage-on-gentoo /var/lib/layman/java-overlay /var/lib/layman/sunrise /usr/local/portage /var/lib/cpan /var/lib/g-octave"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="3dnow 3dnowext 64bit R X Xaw3d a52 aac accessibility acl acpi admin afs alsa amd64 ao apache2 applet archive arpack asf aspell assistant atlas audacious audiofile automap automount bash-completion berkdb blas blast bluetooth boo boost 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 declarative designer devhelp device-mapper dga dia djvu doc dri ds2490 ds9097 ds9097u dv dvb dvd dvdr dvi dynamicplugin eds elf emacs emboss emf encode epiphany evo examples exif expat extensions extra extras ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpx fts3 fuse galago gcj gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp ginac git glade glib glpk gml gmp gmtsuppl gnome gnome-keyring gnome-print gnuplot gnutls gphoto2 gpm grammar graphics graphtft graphviz grass gs gsl gsm gstreamer gtk gudev guile harness hddtemp hdf hdf5 hdri http httpd hvm hwdb iconv icq icu id3 imagemagick imap innodb inotify ipod ipv6 ithreads jabber jadetex java java6 jbig john jpeg jpeg2k kdrive kerberos kpathsea kqemu kvm ladspa lame lapack latex latex3 lcms ldap libffi libgda libnotify libsamplerate lm_sensors lua lzo mad mail maildir mapnik math matroska mkl mmx mmxext mng modules mono motif mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap multilib musicbrainz mysql mysqli nautilus ncurses netcdf netpbm network networking networkmanager nfs nls nntp nptl nptlonly nsplugin ntfs ntp numpy obex objc ocaml ocr octave odbc ogdi ogg ole openexr opengl openmp overview pam pcre pda pdf perl plotutils plugins png podcast policykit portaudio posix postgres postscript pppd preview-latex proj projectx pstricks pulseaudio python python-bindings q16 q32 qemu qhull qt3support qt4 quicktime readline reiserfs reports rle romio rpc rrdcgi rrdtool sage samba sasl science sdk sdl secure-delete semantic-desktop server session sip slang slp smbclient smp sms sndfile snmp soup sox speex spell sql sqlite sse sse2 sse4a ssl subtitles subversion suexec svg svm swig sysfs szip t1lib tcl tcpd tex tex4ht texmacs tgif theora threads thunderbird tidy tiff tk tools truetype udev unicode usb userlocales utempter vaapi video virtualbox vorbis wav webdav webdav-serf webkit wmf wxwidgets xattr xcb xemacs xext xft xine xml xmlreader xmlrpc xorg xpm xulrunner xv xvid xvmc yaml zlib zvbi" 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" 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 cgid 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" CALLIGRA_FEATURES="kexi words flow plan stage tables krita karbon braindump" CAMERAS="canon" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" 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 ubx" 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" PHP_TARGETS="php5-3" QEMU_SOFTMMU_TARGETS="i386 ppc ppc64 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nv 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, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS



root@impala:/root(26)# emerge -pqv =dev-perl/Bio-BigFile-1.06
[ebuild  N    ] dev-perl/Bio-BigFile-1.06

[Comment 1 Juergen Rose 2012-01-01 08:58:26 UTC]

Created attachment 297511 [details]
/var/tmp/portage/dev-perl/Bio-BigFile-1.06/temp/build.log

[Comment 2 Juergen Rose 2012-01-28 12:44:17 UTC]

After installation of ucsc-genome-browser-223 I have now a /usr/lib/jkweb.a.
But Bio-BigFile-1.06 fails now to install with:
...
/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib/jkweb.a(bbiRead.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC
/usr/lib/jkweb.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
error building blib/arch/auto/Bio/DB/BigFile/BigFile.so from lib/Bio/DB/BigFile.o at /usr/lib64/perl5/vendor_perl/5.12.4/ExtUtils/CBuilder/Base.pm line 310.

[Comment 3 Juergen Rose 2012-01-28 15:10:11 UTC]

After upgrade to ucsc-genome-browser-260 /usr/lib/jkweb.a disapeared and 'emerge Bio-BigFile" fails again with the old error.

[Comment 4 Juergen Rose 2012-02-11 16:02:44 UTC]

ping