Boost failed updating 1 target Mauritian girl chat

* The complete build log is located at '/mnt/video/tmp/portage/dev-libs/boost-1.55.0-r1/temp/build.log'.

* The ebuild environment file is located at '/mnt/video/tmp/portage/dev-libs/boost-1.55.0-r1/temp/environment'.

I am trying to compile bcl2fastq on a server where I cannot be root and should be installed in a specific folder (server is under Cent OS 6.5). First I downloaded the tarball: wget ftp://webdata:[email protected]/Downloads/Software/bcl2fastq/bcl2fastq-1.8.4bz2 Then created some variables: export TMP=/tmp export SOURCE=$/bcl2fastq-1.8.4 export BUILD=$/bcl2fastq-1.8.4-build export INSTALL=/software/bcl2fastq/bcl2fastq-1.8.4 Then I extracted the files: cd $ tar xjf /software/bcl2fastq/bcl2fastq-1.8.4bz2 mv bcl2fastq bcl2fastq-1.8.4 Then I ran the configuration: mkdir $ cd $ $/src/configure --prefix=$ But at this step I encounter an error, at 93% of the compilation : Linking CXX executable ../bin/ccmake /software6/apps/buildtools/20140527/bin/ld: CMake Files/ccmake.dir/Curses Dialog/cm Curses Main Form.o: undefined reference to symbol 'keypad' /lib64/5: error adding symbols: DSO missing from command line Do you have any idea to solve the problem? You may need to install these additional Boost libraries. syntax error at /software/bcl2fastq/bcl2fastq-1.8.4/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/line 751, near "$directory qw(ELAND_GENOME)" Global symbol "$self" requires explicit package name at /software/bcl2fastq/bcl2fastq-1.8.4/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/line 753.

Boost version: 1.44.0 Boost include path: /tmp/bcl2fastq-1.8.4-build/opt/bootstrap/include The following Boost libraries could not be found: boost_thread Some (but not all) of the required Boost libraries were found. syntax error at /software/bcl2fastq/bcl2fastq-1.8.4/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/line 747, near "$variable qw(ELAND_FASTQ_FILES_PER_PROCESS)" Global symbol "$variable" requires explicit package name at /software/bcl2fastq/bcl2fastq-1.8.4/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/line 749.

p=141026&postcount=29 but I do not have the root privileges, so any ideas to make it work?

In file included from ../boost/filesystem/path_traits.hpp:23:0, from ../boost/filesystem/path.hpp:25, from ../boost/filesystem/operations.hpp:25, from regression/src/compiler_status.cpp:29: ../boost/system/error_code.hpp: At global scope: ../boost/system/error_code.hpp:2: warning: ‘boost::system::posix_category’ defined but not used [-Wunused-variable] static const error_category & posix_category = generic_category(); ^ ../boost/system/error_code.hpp:2: warning: ‘boost::system::errno_ecat’ defined but not used [-Wunused-variable] static const error_category & errno_ecat = generic_category(); ^ ../boost/system/error_code.hpp:2: warning: ‘boost::system::native_ecat’ defined but not used [-Wunused-variable] static const error_category & native_ecat = system_category(); ^ ...skipped compiler_status.o...

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So, I went to the boost folder, ran the vcvars32and then tried to run the command, c:\boost\boost_1_59_0bjam toolset=msvc-11.0 variant=release threading=multi link=shared define=_BIND_TO_CURRENT_VCLIBS_VERSION and got the response, 'bjam' is not recognized as an internal or external command, So, then I ran the command, t understand why we are using this Linux world crap on a Windows machine with c /cli and dot net available but since I'm stuck with it I'm wondering if anyone can tell me how to get this library built for Visual Studio 2012?

Because it went straight to the Boost compilation : cmake version "cmake version 2.8.4" is already installed at /tmp/bcl2fastq-1.8.4-build/bootstrap/bin/cmake nothing to be done Using installed /tmp/bcl2fastq-1.8.4-build/bootstrap/bin/cmake Do a "make clean" and try again. Probably pretty late in France so we can take this up tomorrow in case no one else comes along with a brilliant answer between now and tomorrow. Global symbol "$barcode" requires explicit package name at /software/bcl2fastq/bcl2fastq-1.8.4/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/line 753.

Actually I am just at the step of the configure script. I am sure that it is not the bzip2 library that is problematic here, but something with boost thread and GCC version. I tried the oldest gcc on my system, it did not work : C compiler on this system is: /compilers/gcc/4.6/bin/gcc C compiler on this system is: /compilers/gcc/4.6/bin/g And in the end : CMake Error at cmake/cxx Configure.cmake:84 (message): No support for bzip2 compression With a clean install : Decompressing /tmp/bcl2fastq-1.8.4/src/../redist/cmake-2.8.4gz --------------------------------------------- CMake 2.8.4, Copyright 2000-2009 Kitware, Inc. Global symbol "$reference" requires explicit package name at /software/bcl2fastq/bcl2fastq-1.8.4/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/line 753.

Portage 2.2.9-r1 (default/linux/amd64/13.0/desktop/kde, gcc-4.8.2, glibc-2.18-r1, 3.12.8-gentoo x86_64) ================================================================= System Settings ================================================================= System uname: [email protected]_2.50GHz-with-gentoo-2.2 Ki B Mem: 8081688 total, 368300 free Ki B Swap: 9767484 total, 9767412 free Timestamp of tree: Tue, 0000 ld GNU ld (GNU Binutils) 2.24 app-shells/bash: 4.2_p45-r1 dev-java/java-config: 2.2.0 dev-lang/python: 2.7.6, 3.3.4 dev-util/cmake: 2.8.12.2 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: 1.11.6, 1.14.1 sys-devel/binutils: 2.24-r2 sys-devel/gcc: 4.8.2 sys-devel/gcc-config: 1.8 sys-devel/libtool: 2.4.2 sys-devel/make: 4.0-r1 sys-kernel/linux-headers: 3.13 (virtual/os-headers) sys-libs/glibc: 2.18-r1 Repositories: gentoo bumblebee x-my ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -O2 -pipe -ggdb" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg//usr/share/themes/oxygen-gtk/gtk-2.0" CONFIG_PROTECT_MASK="/etc//etc/env.d /etc/fonts//etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" CXXFLAGS="-march=native -O2 -pipe -ggdb" 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 userpriv usersandbox usersync" FFLAGS="-O2 -pipe" GENTOO_MIRRORS=" rsync://mirror.uk/gentoo/" LANG="en_GB.utf8" 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/video/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/var/lib/layman/bumblebee /usr/local/my" USE="X a52 aac acl acpi alsa amd64 berkdb bluetooth branding bzip2 cairo cdda cddb cdr cli consolekit cracklib crypt cups cxx dbus declarative demosaic djvu dri dts dv dvd dvdr ebook embedded emboss encode exif fam ffmpeg firefox flac fortran frei0r gdbm gde gif gles2 gpm gtk iconv icu ios ipv6 java jpeg kde kdenlive kipi lcms ldap libkms libnotify lm_sensors mad melt minizip mlt mmx mng modules mp3 mp4 mpeg mysql ncurses nls nptl nsplugin ogg opengl openmp opus pam pango pcre pdf phonon plasma png policykit ppds qt3support qt4 readline reports scanner script sdl semantic-desktop session smp sna spell sqlite sse sse2 sse3 sse41 sse42 ssl ssse3 startup-notification svg tcpd threads tiff tools truetype udev udisks unicode upower usb vaapi vcd vorbis wxwidgets x264 xcb xcomposite xinerama xml xmp xscreensaver xv xvid 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="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" 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" 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="evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="pl en en_GB" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" RUBY_TARGETS="ruby19 ruby20" USERLAND="GNU" VIDEO_CARDS="nvidia intel" 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 ================================================================= dev-libs/boost-1.55.0-r1 was built with the following: USE="icu nls python threads -context -debug -doc -mpi -static-libs -tools" PYTHON_TARGETS="python2_7 python3_3 -python2_6 -python3_2" CXXFLAGS="-march=native -O2 -pipe -ggdb -std=gnu 98"Can you file this bug at Gentoo Bugzilla and provide the complete build log to them?

It might be a parallel build issue as suggested but it might very well be the that the error has been cut off the message; to see if there is an error, grep for FYI, mu machine also failed to emerge dev-libs/boost-1.55.0-r1, but after removing MAKEOPTS="-j5" from my emerge succeeded. (I'm using gcc-4.8.2 and glibc-2.19) Cheers,_________________Freedom works. Linux, by Gentoo FYI, mu machine also failed to emerge dev-libs/boost-1.55.0-r1, but after removing MAKEOPTS="-j5" from my emerge succeeded. (I'm using gcc-4.8.2 and glibc-2.19)There are many ways to fail.

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