>>> Emerging (118 of 121) sci-biology/bioperl-1.6.9::gentoo * BioPerl-1.6.901.tar.gz SHA256 SHA512 WHIRLPOOL size ;-) ... [ ok ] >>> Unpacking source... >>> Unpacking BioPerl-1.6.901.tar.gz to /mnt/1TB/var/tmp/portage/sci-biology/bioperl-1.6.9/work >>> Source unpacked in /mnt/1TB/var/tmp/portage/sci-biology/bioperl-1.6.9/work >>> Preparing source in /mnt/1TB/var/tmp/portage/sci-biology/bioperl-1.6.9/work/BioPerl-1.6.901 ... >>> Source prepared. >>> Configuring source in /mnt/1TB/var/tmp/portage/sci-biology/bioperl-1.6.9/work/BioPerl-1.6.901 ... * Using Module::Build * perl Build.PL --installdirs=vendor --libdoc= --destdir=/mnt/1TB/var/tmp/portage/sci-biology/bioperl-1.6.9/image/ --create_packlist=0 Checking prerequisites... requires: ! Data::Stag is not installed recommends: * Error is not installed Checking optional features... EntrezGene............disabled requires: ! Bio::ASN1::EntrezGene is not installed Pg Tests..............disabled requires: ! DBD::Pg is not installed ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation Run 'Build installdeps' to install missing prerequisites. ############################# WARNING ############################# Bio::ASN1::EntrezGene not found. This is an *optional* module; however, because it has a circular dependency with BioPerl we do not include it on our list of recommended modules. If you require EntrezGene functionality, you can install Bio::ASN1::EntrezGene after BioPerl has finished installing. ############################# WARNING #############################
hi, can you attach your emerge --info and the full build.log.
# emerge -pv bioperl [ebuild R ] sci-biology/bioperl-1.6.9::gentoo USE="db network run sqlite -graphviz -minimal" 0 KiB # emerge --info Portage 2.2.18 (python 2.7.5-final-0, default/linux/amd64/13.0, gcc-4.9.2, glibc-2.20-r2, 3.10.72-default-pciehp x86_64) ================================================================= System uname: Linux-3.10.72-default-pciehp-x86_64-Intel-R-_Core-TM-_i7-2640M_CPU_@_2.80GHz-with-gentoo-2.2 KiB Mem: 16368868 total, 2782788 free KiB Swap: 4998972 total, 4998972 free Timestamp of repository gentoo: Tue, 07 Apr 2015 18:30:01 +0000 sh bash 4.3_p33-r2 ld GNU ld (Gentoo 2.25 p1.0) 2.25 app-shells/bash: 4.3_p33-r2::gentoo dev-java/java-config: 2.2.0::gentoo dev-lang/perl: 5.20.2::gentoo dev-lang/python: 2.7.5-r4::gentoo, 3.2.5-r3::gentoo dev-util/cmake: 3.1.0::gentoo dev-util/pkgconfig: 0.28-r1::gentoo sys-apps/baselayout: 2.2::gentoo sys-apps/openrc: 0.13.11::gentoo sys-apps/sandbox: 2.6-r1::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69::gentoo sys-devel/automake: 1.11.6::gentoo, 1.12.6::gentoo, 1.13.4::gentoo, 1.14::gentoo sys-devel/binutils: 2.25::gentoo sys-devel/gcc: 4.3.6-r1::gentoo, 4.4.7::gentoo, 4.6.4::gentoo, 4.7.4::gentoo, 4.8.4::gentoo, 4.9.2::gentoo sys-devel/gcc-config: 1.8::gentoo sys-devel/libtool: 2.4.4::gentoo sys-devel/make: 4.1-r1::gentoo sys-kernel/linux-headers: 3.19::gentoo (virtual/os-headers) sys-libs/glibc: 2.20-r2::gentoo Repositories: gentoo location: /mnt/1TB/usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 haskell location: /var/lib/layman/haskell masters: gentoo priority: 0 science location: /home/mmokrejs/proj/sci masters: gentoo priority: 1 x-portage location: /usr/local/portage masters: gentoo priority: 2 layman location: /var/lib/layman masters: gentoo priority: 3 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA dlj-1.1 sun-bcla-java-vm Oracle-BCLA-JavaSE IBM-J1.6 skype-eula Nero-EULA-US AdobeFlash-10.3 skype-4.0.0.7-copyright AdobeFlash-11.x" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -maes -mpclmul -mpopcnt -mavx -march=native" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/easy-rsa /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.2/conf /var/bind /var/lib/hsqldb /var/spool/torque" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.4/ext-active/ /etc/php/apache2-php5.5/ext-active/ /etc/php/apache2-php5.6/ext-active/ /etc/php/cgi-php5.4/ext-active/ /etc/php/cgi-php5.5/ext-active/ /etc/php/cgi-php5.6/ext-active/ /etc/php/cli-php5.4/ext-active/ /etc/php/cli-php5.5/ext-active/ /etc/php/cli-php5.6/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="-O2 -pipe -maes -mpclmul -mpopcnt -mavx -march=native" DISTDIR="/mnt/1TB/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news nostrip parallel-fetch preserve-libs protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="rsync://ftp.fi.muni.cz/pub/linux/gentoo/ rsync://gentoo.mirror.dkm.cz/gentoo/ ftp://gentoo.mirror.web4u.cz/" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j2" 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="/mnt/1TB/var/tmp" USE="X acpi alsa amd64 amr apache apache2 apulse avx berkdb bindist bluetooth boost bzip2 cairo cgi cli cracklib crypt cryptlib cups cxx dbus device-mapper dhcp directfb dri emboss encode fax fbcon ffmpeg flac fontconfig fortran gbm gd gdbm geoip gimp gnutls gpm gtk gudev hal hpijs hwdb iconv id3tag imaging innodb java jce jpeg jpg keymap ladspa lapack laptop lcms libnotify lm_sensors mad mmx mmxext modules mpi mpich2 multilib mysql ncurses nfs nls nptl nptlonly nsplugin ntfsprogs ocr ogg opengl openmp pam parport pcre pdf perl php png ppds pppd python readline rendering resolvconf scanner server session slideshow sndfile sqlite sse sse2 sse3 sse4_1 sse4_2 ssl ssse3 suexec svg syslog tcl tcpd threads tiff tk truetype udev unicode usb vim-syntax wavpack wifi x11 xml xorg 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="alias authz_host auth_basic auth_digest cgi cgid deflate dir env filter include info mem_cache mime mime_magic negotiation remoteip setenvif status userdir vhost_alias rewrite usertrack cache file_cache disk_cache charset_lite log_config log_forensic" 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" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en en_US en_GB cs cz" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-4 php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" RUBY_TARGETS="ruby19 ruby20" USERLAND="GNU" VIDEO_CARDS="vesa vmware fbdev intel i915" 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" USE_PYTHON="2.7" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Created attachment 400772 [details] build.log
+ 08 Apr 2015; Justin Lecher <jlec@gentoo.org> bioperl-1.6.9.ebuild, + bioperl-9999-r1.ebuild, metadata.xml: + Add missing deps, bug #545472 +
