Bug 383789

Summary:	sci-biology/ncbi-tools++-2010.06.15-r1: libmzXML.so: undefined reference to `ncbi::CMemberInfo::SetNoPrefix()'
Product:	Gentoo Linux	Reporter:	Martin Mokrejš <mmokrejs>
Component:	Current packages	Assignee:	Gentoo Science Biology related packages <sci-biology>
Status:	RESOLVED OBSOLETE
Severity:	normal	CC:	kredba, weaver
Priority:	Normal
Version:	unspecified
Hardware:	All
OS:	Linux
Whiteboard:
Package list:		Runtime testing required:	---
Bug Depends on:
Bug Blocks:	457936

Description Martin Mokrejš 2011-09-20 08:34:45 UTC

/usr/bin/i686-pc-linux-gnu-g++  -c  -Wall -Wno-format-y2k  -pthread -O2 -march=pentium4m -mmmx -msse -msse2 -pipe -fno-strict-aliasing -ggdb -fPIC  -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64  -D_MT -D_REENTRANT -D_THREAD_SAFE -I/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/inc -I/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/include  -I/usr/include/libxml2  /var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/src/app/mshdf5/MzXmlReader.cpp -o MzXmlReader.o 
/usr/bin/i686-pc-linux-gnu-g++  -pthread -Wl,-O1 -Wl,--as-needed -O -Wl,-E  mzXML2hdf5.o MzXmlReader.o   -Wl,-rpath,/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/image//usr/lib/ncbi-tools++ -Wl,-rpath-link,/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib -L/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib -lmshdf5 -lmzXML -lxmlwrapp -lgeneral -lxregexp -lxconnect -lxser -lxutil -lxncbi -lxcompress -lpcre  -lz  -lbz2  -llzo2  -lxml2  -lhdf5_cpp -lhdf5 -lrt -lm  -lpthread -o mzXML2hdf5 
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::CMemberInfo::SetNoPrefix()'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::CSerialObject::DebugDump(ncbi::CDebugDumpContext, unsigned int) const'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmshdf5.so: undefined reference to `ncbi::MSerial_Xml(std::basic_ios<char, std::char_traits<char> >&)'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::AddMember(ncbi::CClassTypeInfoBase*, char const*, void const*, ncbi::CTypeInfo const* (*)(ncbi::CTypeInfo const*), ncbi::CTypeInfo const* (*)())'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::CMemberInfo::SetOptional()'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::CEnumeratedTypeValues::CEnumeratedTypeValues(char const*, bool)'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::RegisterEnumTypeValuesObject(ncbi::CEnumeratedTypeValues*)'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::CStdTypeInfo<bool>::GetTypeInfo()'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::AddMember(ncbi::CClassTypeInfoBase*, char const*, void const*, ncbi::CTypeInfo const* (*)())'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::CSerialObject::Assign(ncbi::CSerialObject const&, ncbi::ESerialRecursionMode)'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::AddMember(ncbi::CClassTypeInfoBase*, char const*, void const*, ncbi::CTypeInfo const*)'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::AddMember(ncbi::CClassTypeInfoBase*, char const*, void const*, ncbi::CTypeInfo const* (*)(ncbi::CTypeInfo const*), ncbi::CTypeInfo const* (*)(ncbi::CTypeInfo const*), ncbi::CTypeInfo const* (*)())'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::CPointerTypeInfo::SetFunctions(void* (*)(ncbi::CPointerTypeInfo const*, void*), void (*)(ncbi::CPointerTypeInfo const*, void*, void*))'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::CClassInfoHelperBase::CreateClassInfo(char const*, unsigned int, ncbi::CObject const*, void* (*)(ncbi::CTypeInfo const*, ncbi::CObjectMemoryPool*), std::type_info const&, std::type_info const* (*)(void const*))'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::CMemberInfo::SetDefault(void const*)'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::CStdTypeInfo<double>::GetTypeInfo()'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::CStdTypeInfo<int>::GetTypeInfo()'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::CStlOneArgTemplate::CStlOneArgTemplate(unsigned int, ncbi::CTypeInfo const*, bool)'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::CPointerTypeInfo::CPointerTypeInfo(unsigned int, ncbi::CTypeInfo const*)'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::CSerialObject::Equals(ncbi::CSerialObject const&, ncbi::ESerialRecursionMode) const'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::CContainerTypeInfo::SetConstIteratorFunctions(bool (*)(ncbi::CContainerTypeInfo::CConstIterator&), void (*)(ncbi::CContainerTypeInfo::CConstIterator&), void (*)(ncbi::CContainerTypeInfo::CConstIterator&, ncbi::CContainerTypeInfo::CConstIterator const&), bool (*)(ncbi::CContainerTypeInfo::CConstIterator&), void const* (*)(ncbi::CContainerTypeInfo::CConstIterator const&))'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmshdf5.so: undefined reference to `ncbi::operator>>(std::basic_istream<char, std::char_traits<char> >&, ncbi::CSerialObject&)'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::CSerialObject::~CSerialObject()'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::CMemberInfo::SetNotag()'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::CStlClassInfoUtil::Get_list(ncbi::CTypeInfo const*, ncbi::CTypeInfo* (*)(ncbi::CTypeInfo const*))'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::GetTypeInfoMutex()'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `typeinfo for ncbi::CSerialObject'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::CMemberInfo::SetAttlist()'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::CTypeInfo::SetNamespaceName(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::CStdTypeInfo<bool>::GetTypeInfoNullBool()'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::CEnumeratedTypeInfo::CEnumeratedTypeInfo(unsigned int, ncbi::CEnumeratedTypeValues const*, bool)'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::CContainerTypeInfo::SetCountFunctions(unsigned int (*)(ncbi::CContainerTypeInfo const*, void const*), void (*)(ncbi::CContainerTypeInfo const*, void*, unsigned int))'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::CMemberInfo::SetSetFlag(unsigned int const*)'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::CContainerTypeInfo::SetAddElementFunctions(void* (*)(ncbi::CContainerTypeInfo const*, void*, void const*, ncbi::ESerialRecursionMode), void* (*)(ncbi::CContainerTypeInfo const*, void*, ncbi::CObjectIStream&))'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmshdf5.so: undefined reference to `ncbi::CSerialObject::ThrowUnassigned(unsigned int) const'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::RegisterTypeInfoObject(ncbi::CTypeInfo*)'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::CEnumeratedTypeValues::AddValue(char const*, int)'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::CSerialObject::CSerialObject()'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::CStlClassInfoUtil::Get_CRef(ncbi::CTypeInfo const*, ncbi::CTypeInfo* (*)(ncbi::CTypeInfo const*))'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::CStdTypeInfo<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >::GetTypeInfo()'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::CContainerTypeInfo::SetIteratorFunctions(bool (*)(ncbi::CContainerTypeInfo::CIterator&), void (*)(ncbi::CContainerTypeInfo::CIterator&), void (*)(ncbi::CContainerTypeInfo::CIterator&, ncbi::CContainerTypeInfo::CIterator const&), bool (*)(ncbi::CContainerTypeInfo::CIterator&), void* (*)(ncbi::CContainerTypeInfo::CIterator const&), bool (*)(ncbi::CContainerTypeInfo::CIterator&), void (*)(ncbi::CContainerTypeInfo::CIterator&))'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::CClassTypeInfo::SetRandomOrder(bool)'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::CStlOneArgTemplate::SetMemFunctions(void* (*)(ncbi::CTypeInfo const*, ncbi::CObjectMemoryPool*), bool (*)(void const*), void (*)(void*))'
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::SetModuleName(ncbi::CTypeInfo*, char const*)'
collect2: ld returned 1 exit status
make[7]: *** [mzXML2hdf5] Error 1
make[7]: Leaving directory `/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/build/app/mshdf5'

Comment 1 Martin Mokrejš 2011-09-20 08:35:52 UTC

# emerge --info =sci-biology/ncbi-tools++-2010.06.15-r1
Portage 2.1.10.10 (default/linux/x86/10.0/desktop, gcc-4.5.3, glibc-2.13-r4, 3.0.4 i686)
=================================================================
                        System Settings
=================================================================
System uname: Linux-3.0.4-i686-Mobile_Intel-R-_Pentium-R-_4_-_M_CPU_1.80GHz-with-gentoo-2.0.3
Timestamp of tree: Mon, 19 Sep 2011 14:45:01 +0000
distcc 3.1 i686-pc-linux-gnu [disabled]
app-shells/bash:          4.2_p10
dev-java/java-config:     2.1.11-r3
dev-lang/python:          2.5.4-r4, 2.6.7-r2, 2.7.2-r2, 3.1.4-r2, 3.2-r2
dev-util/cmake:           2.8.5-r2
dev-util/pkgconfig:       0.26
sys-apps/baselayout:      2.0.3
sys-apps/openrc:          0.8.3-r1
sys-apps/sandbox:         2.5
sys-devel/autoconf:       2.13::<unknown repository>, 2.68
sys-devel/automake:       1.4_p6-r1, 1.5-r1, 1.6.3-r1, 1.7.9-r2, 1.8.5-r4, 1.9.6-r3, 1.10.3, 1.11.1-r1
sys-devel/binutils:       2.21.1-r1
sys-devel/gcc:            3.3.6-r1, 4.2.4-r1, 4.3.6-r1, 4.4.6-r1, 4.5.3-r1
sys-devel/gcc-config:     1.4.1-r1
sys-devel/libtool:        2.4-r1
sys-devel/make:           3.81-r2
sys-kernel/linux-headers: 2.6.38 (virtual/os-headers)
sys-libs/glibc:           2.13-r4
Repositories: gentoo x-portage science
ACCEPT_KEYWORDS="x86 ~x86"
ACCEPT_LICENSE="* -@EULA dlj-1.1 sun-bcla-java-vm Nero-EULA-US skype-eula AdobeFlash AdobeFlash-10 AdobeFlash-10.1 PUEL Oracle-BCLA-JavaSE"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-O2 -march=pentium4m -mmmx -msse -msse2 -pipe -fno-strict-aliasing -ggdb"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt /usr/share/openvpn/easy-rsa /var/bind /var/lib/hsqldb /var/vpopmail/etc"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.2/ext-active/ /etc/php/apache2-php5.3/ext-active/ /etc/php/cgi-php5.2/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cli-php5.2/ext-active/ /etc/php/cli-php5.3/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 -march=pentium4m -mmmx -msse -msse2 -pipe -fno-strict-aliasing -ggdb"
DISTDIR="/usr/portage/distfiles"
FEATURES="assume-digests binpkg-logs distlocks ebuild-locks fixlafiles fixpackages news nostrip parallel-fetch protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS=""
GENTOO_MIRRORS="http://gentoo.mirror.web4u.cz"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LINGUAS="en cs cz"
MAKEOPTS="-j2"
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="/usr/local/portage /home/mmokrejs/proj/sci"
SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage"
USE="32bit 7zip R X Xaw3d a52 aac aalib ace acl acpi alsa amr amrnb amrwb apache apache2 apng audacious audiofile bash-completion bcmath berkdb blas bluetooth boost branding bzip2 cairo caps cblas cdda cddb cdparanoia cdr cgi clamav cli colordiff compress consolekit cpio cracklib crypt cscope css ctype cups curl curlwrappers cxx dbi dbus dga dhcp dia directfb djbfft dlz dri dts dv dvb dvd dvdr dvdread emboss emf enblend encode enscript exif expat faad fam fame fat fbcon ffmpeg fftw firefox flac flash fontconfig fortran fpx ftp gcj gd gdbm gdu ggi gif gimp gimpprint glibc-compat20 glibc-omitfp glut gmp gnuplot gnutls gpgme gphoto2 gpm graphviz gs gsl gsm gtk gtkhtml hdf hdf5 hp2xx i8x0 iconv icu id3 id3tag ieee1394 imagemagick imlib inifile innodb ithreads jack java javascript jbig jce jikes jpeg jpeg2k kdtree kerberos ladspa lame lapack laptop largefile lcms leim libcaca libnotify libwww live lzo lzw mad maildir matroska mhash mikmod mime ming mjpeg mmap mmx mng mod_python modperl modplug modules motif mozilla moznoirc mp2 mp3 mp4 mpeg mplayer mudflap mule musepack mxdatetime mysql mysqli nat ncurses netcdf netpbm network nls nntp nptl nptlonly nsplugin ntfs numeric objc ogg opengl openmp openssl pam pango parport pcmcia pcntl pcre pdf perl php plotutils plugin png pnm policykit postproc postscript ppds pppd procmail pymol python qt3support qt4 quicktime rar raw readline recode reiserfs romio rpm samba sasl scanner scp sdl seamonkey server session sftp sift slp smime sndfile soap sockets spell sqlite srt sse sse2 ssl startup-notification static-libs subtitles subversion svg svgz sysfs sysvipc t1lib tcl tcpd theora tidy tiff tk transcode truetype udev unicode urandom usb userlocales utils uuencode v4l v4l2 vcd vhook vim-syntax vim-with-x vorbis wavpack wifi win32codecs wmf wxwindows x264 x86 xanim xcb xcf xfs xft xinerama xinetd xml xorg xpm xsl xslt xulrunner xv xvid xvmc yv12 zip zlib" ALSA_CARDS="intel-8x0m" 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 cgi cgid dbd deflate dir disk_cache env expires ext_filter file_cache filter headers icu ident imagemap include info log_config mem_cache mime mime_magic php rewrite setenvif speling status unique_id userdir usertrack vhost_alias negotiation" CALLIGRA_FEATURES="kexi words flow plan stage tables krita karbon braindump" CAMERAS="ptp2" 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="en cs cz" PHP_TARGETS="php-5-3" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="radeon 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, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

# emerge -pqv =sci-biology/ncbi-tools++-2010.06.15-r1
[ebuild     U ] sci-biology/ncbi-tools++-2010.06.15-r1 [2010.06.15] USE="mysql sqlite"

Comment 2 Justin Lecher (RETIRED) gentoo-dev

2011-09-20 08:43:04 UTC


*** This bug has been marked as a duplicate of bug 383721 ***

Comment 3 Martin Mokrejš 2011-12-27 16:05:46 UTC

No, I am still getting this error and I don't see why a

/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC453-ReleaseMTDLL/lib/libmzXML.so: undefined reference to `ncbi::CMemberInfo
::SetNoPrefix()'


error is a dupe of libpng15 issue in bug #383721. Please re-open.

Comment 4 David Kredba 2012-03-18 10:50:56 UTC

Keeping only "pkl2hdf5 mshdf2mzXML" for APP_PROJ in /var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/GCC463-ReleaseMTDLL64/build/app/mshdf5/Makefile
allows the package to build.

Comment 5 Robin Johnson archtester

2014-08-03 20:35:19 UTC

ncbi-tools++ was removed from the tree it seems, so these bugs aren't relevant anymore.