usr/include/boost/archive/binary_iarchive.hpp:57:1: required by substitution of ‘template<class Serializable> typename boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, Serializable>::type boost::archive::detail::instantiate_ptr_serialization(Serializable*, boost::archive::binary_iarchive*, boost::archive::detail::adl_tag) [with Serializable = AbundanceGroup]’ /usr/include/boost/serialization/export.hpp:132:58: required from ‘void boost::archive::detail::extra_detail::guid_initializer<T>::export_guid(mpl_::false_) const [with T = AbundanceGroup; mpl_::false_ = mpl_::bool_<false>]’ /usr/include/boost/serialization/export.hpp:142:61: required from ‘const boost::archive::detail::extra_detail::guid_initializer<T>& boost::archive::detail::extra_detail::guid_initializer<T>::export_guid() const [with T = AbundanceGroup]’ /var/tmp/portage/sci-biology/cufflinks-2.2.1-r1/work/cufflinks-2.2.1/src/abundances.cpp:5162:1: required from here /usr/include/boost/smart_ptr/shared_ptr.hpp:408:5: note: template<class Y> boost::shared_ptr<T>::shared_ptr(const boost::weak_ptr<Y>&, boost::detail::sp_nothrow_tag) shared_ptr( weak_ptr<Y> const & r, boost::detail::sp_nothrow_tag ) ^ /usr/include/boost/smart_ptr/shared_ptr.hpp:408:5: note: template argument deduction/substitution failed: In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.4/include/g++-v4/bits/stl_algobase.h:64:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.4/include/g++-v4/vector:60, from /var/tmp/portage/sci-biology/cufflinks-2.2.1-r1/work/cufflinks-2.2.1/src/abundances.h:17, from /var/tmp/portage/sci-biology/cufflinks-2.2.1-r1/work/cufflinks-2.2.1/src/abundances.cpp:16: /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.4/include/g++-v4/bits/stl_pair.h:119:39: note: ‘const boost::shared_ptr<const EmpDist>’ is not derived from ‘const boost::weak_ptr<Y>’ : first(__p.first), second(__p.second) { } ^ In file included from /usr/include/boost/shared_ptr.hpp:17:0, from /var/tmp/portage/sci-biology/cufflinks-2.2.1-r1/work/cufflinks-2.2.1/src/hits.h:19, from /var/tmp/portage/sci-biology/cufflinks-2.2.1-r1/work/cufflinks-2.2.1/src/abundances.h:23, from /var/tmp/portage/sci-biology/cufflinks-2.2.1-r1/work/cufflinks-2.2.1/src/abundances.cpp:16: /usr/include/boost/smart_ptr/shared_ptr.hpp:399:14: note: template<class Y> boost::shared_ptr<T>::shared_ptr(const boost::weak_ptr<Y>&) explicit shared_ptr( weak_ptr<Y> const & r ): pn( r.pn ) // may throw ^ /usr/include/boost/smart_ptr/shared_ptr.hpp:399:14: note: template argument deduction/substitution failed: In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.4/include/g++-v4/bits/stl_algobase.h:64:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.4/include/g++-v4/vector:60, from /var/tmp/portage/sci-biology/cufflinks-2.2.1-r1/work/cufflinks-2.2.1/src/abundances.h:17, from /var/tmp/portage/sci-biology/cufflinks-2.2.1-r1/work/cufflinks-2.2.1/src/abundances.cpp:16: /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.4/include/g++-v4/bits/stl_pair.h:119:39: note: ‘const boost::shared_ptr<const EmpDist>’ is not derived from ‘const boost::weak_ptr<Y>’ : first(__p.first), second(__p.second) { } ^ In file included from /usr/include/boost/shared_ptr.hpp:17:0, from /var/tmp/portage/sci-biology/cufflinks-2.2.1-r1/work/cufflinks-2.2.1/src/hits.h:19, from /var/tmp/portage/sci-biology/cufflinks-2.2.1-r1/work/cufflinks-2.2.1/src/abundances.h:23, from /var/tmp/portage/sci-biology/cufflinks-2.2.1-r1/work/cufflinks-2.2.1/src/abundances.cpp:16: /usr/include/boost/smart_ptr/shared_ptr.hpp:373:41: note: template<class Y, class D, class A> boost::shared_ptr<T>::shared_ptr(Y*, D, A) template<class Y, class D, class A> shared_ptr( Y * p, D d, A a ): px( p ), ^ /usr/include/boost/smart_ptr/shared_ptr.hpp:373:41: note: template argument deduction/substitution failed: In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.4/include/g++-v4/bits/stl_algobase.h:64:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.4/include/g++-v4/vector:60, from /var/tmp/portage/sci-biology/cufflinks-2.2.1-r1/work/cufflinks-2.2.1/src/abundances.h:17, from /var/tmp/portage/sci-biology/cufflinks-2.2.1-r1/work/cufflinks-2.2.1/src/abundances.cpp:16: /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.4/include/g++-v4/bits/stl_pair.h:119:39: note: mismatched types ‘Y*’ and ‘boost::shared_ptr<const EmpDist>’ : first(__p.first), second(__p.second) { } ^ In file included from /usr/include/boost/shared_ptr.hpp:17:0, from /var/tmp/portage/sci-biology/cufflinks-2.2.1-r1/work/cufflinks-2.2.1/src/hits.h:19, from /var/tmp/portage/sci-biology/cufflinks-2.2.1-r1/work/cufflinks-2.2.1/src/abundances.h:23, from /var/tmp/portage/sci-biology/cufflinks-2.2.1-r1/work/cufflinks-2.2.1/src/abundances.cpp:16: /usr/include/boost/smart_ptr/shared_ptr.hpp:358:32: note: template<class Y, class D> boost::shared_ptr<T>::shared_ptr(Y*, D) template<class Y, class D> shared_ptr( Y * p, D d ): px( p ), pn( p, d ) ^ /usr/include/boost/smart_ptr/shared_ptr.hpp:358:32: note: template argument deduction/substitution failed: In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.4/include/g++-v4/bits/stl_algobase.h:64:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.4/include/g++-v4/vector:60, from /var/tmp/portage/sci-biology/cufflinks-2.2.1-r1/work/cufflinks-2.2.1/src/abundances.h:17, from /var/tmp/portage/sci-biology/cufflinks-2.2.1-r1/work/cufflinks-2.2.1/src/abundances.cpp:16: /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.4/include/g++-v4/bits/stl_pair.h:119:39: note: mismatched types ‘Y*’ and ‘boost::shared_ptr<const EmpDist>’ : first(__p.first), second(__p.second) { } ^ In file included from /usr/include/boost/shared_ptr.hpp:17:0, from /var/tmp/portage/sci-biology/cufflinks-2.2.1-r1/work/cufflinks-2.2.1/src/hits.h:19, from /var/tmp/portage/sci-biology/cufflinks-2.2.1-r1/work/cufflinks-2.2.1/src/abundances.h:23, from /var/tmp/portage/sci-biology/cufflinks-2.2.1-r1/work/cufflinks-2.2.1/src/abundances.cpp:16: /usr/include/boost/smart_ptr/shared_ptr.hpp:347:14: note: template<class Y> boost::shared_ptr<T>::shared_ptr(Y*) explicit shared_ptr( Y * p ): px( p ), pn() // Y must be complete ^ /usr/include/boost/smart_ptr/shared_ptr.hpp:347:14: note: template argument deduction/substitution failed: In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.4/include/g++-v4/bits/stl_algobase.h:64:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.4/include/g++-v4/vector:60, from /var/tmp/portage/sci-biology/cufflinks-2.2.1-r1/work/cufflinks-2.2.1/src/abundances.h:17, from /var/tmp/portage/sci-biology/cufflinks-2.2.1-r1/work/cufflinks-2.2.1/src/abundances.cpp:16: /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.4/include/g++-v4/bits/stl_pair.h:119:39: note: mismatched types ‘Y*’ and ‘boost::shared_ptr<const EmpDist>’ : first(__p.first), second(__p.second) { } ^ In file included from /usr/include/boost/shared_ptr.hpp:17:0, from /var/tmp/portage/sci-biology/cufflinks-2.2.1-r1/work/cufflinks-2.2.1/src/hits.h:19, from /var/tmp/portage/sci-biology/cufflinks-2.2.1-r1/work/cufflinks-2.2.1/src/abundances.h:23, from /var/tmp/portage/sci-biology/cufflinks-2.2.1-r1/work/cufflinks-2.2.1/src/abundances.cpp:16: /usr/include/boost/smart_ptr/shared_ptr.hpp:334:5: note: boost::shared_ptr<T>::shared_ptr() [with T = void] shared_ptr() BOOST_NOEXCEPT : px( 0 ), pn() // never throws in 1.30+ ^ /usr/include/boost/smart_ptr/shared_ptr.hpp:334:5: note: candidate expects 0 arguments, 1 provided /usr/include/boost/smart_ptr/shared_ptr.hpp:323:25: note: boost::shared_ptr<void>::shared_ptr(const boost::shared_ptr<void>&) template<class T> class shared_ptr ^ /usr/include/boost/smart_ptr/shared_ptr.hpp:323:25: note: no known conversion for argument 1 from ‘const boost::shared_ptr<const EmpDist>’ to ‘const boost::shared_ptr<void>&’ Makefile:1616: recipe for target 'abundances.o' failed make[2]: *** [abundances.o] Error 1 make[2]: Leaving directory '/var/tmp/portage/sci-biology/cufflinks-2.2.1-r1/work/cufflinks-2.2.1_build/src' Makefile:390: recipe for target 'all-recursive' failed make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory '/var/tmp/portage/sci-biology/cufflinks-2.2.1-r1/work/cufflinks-2.2.1_build' Makefile:330: recipe for target 'all' failed make: *** [all] Error 2 * ERROR: sci-biology/cufflinks-2.2.1-r1::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/cufflinks-2.2.1-r1::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/cufflinks-2.2.1-r1::gentoo'`. * The complete build log is located at '/var/log/portage/sci-biology:cufflinks-2.2.1-r1:20150105-203006.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/cufflinks-2.2.1-r1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/cufflinks-2.2.1-r1/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/cufflinks-2.2.1-r1/work/cufflinks-2.2.1_build' * S: '/var/tmp/portage/sci-biology/cufflinks-2.2.1-r1/work/cufflinks-2.2.1' * GNU info directory index is up-to-date. !!! existing preserved libs: >>> package: net-libs/gnutls-2.12.23-r6 * - /usr/lib64/libgnutls.so.28 * - /usr/lib64/libgnutls.so.28.41.3 * used by /usr/lib64/gnutls-0.1.5/ghc-7.8.4/libHSgnutls-0.1.5-ghc7.8.4.so (dev-haskell/gnutls-0.1.5) Use emerge @preserved-rebuild to rebuild packages using these libraries * IMPORTANT: config file '/etc/ppp/options' needs updating. * See the CONFIGURATION FILES section of the emerge * man page to learn how to update config files. This chroot image is located at a hardened amd64 host. Portage 2.2.15 (python 2.7.9-final-0, default/linux/amd64/13.0, gcc-4.8.4, glibc-2.20-r1, 3.17.7-hardened-r1 x86_64) ================================================================= System uname: Linux-3.17.7-hardened-r1-x86_64-Intel-R-_Core-TM-_i7-3770_CPU_@_3.40GHz-with-gentoo-2.2 KiB Mem: 16166924 total, 1334628 free KiB Swap: 16777212 total, 16760864 free Timestamp of tree: Mon, 05 Jan 2015 17:45:01 +0000 sh bash 4.3_p33 ld GNU ld (Gentoo 2.24 p1.4) 2.24 app-shells/bash: 4.3_p33 dev-lang/perl: 5.20.1-r4 dev-lang/python: 2.7.9-r1, 3.3.5-r1 dev-util/cmake: 3.0.2 dev-util/pkgconfig: 0.28-r2 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.13.6 sys-apps/sandbox: 2.6-r1 sys-devel/autoconf: 2.69 sys-devel/automake: 1.9.6-r4, 1.11.6-r1, 1.14.1 sys-devel/binutils: 2.24-r3 sys-devel/gcc: 4.8.4 sys-devel/gcc-config: 1.8 sys-devel/libtool: 2.4.4 sys-devel/make: 4.1-r1 sys-kernel/linux-headers: 3.18 (virtual/os-headers) sys-libs/glibc: 2.20-r1 Repositories: gentoo ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt /usr/share/qpsmtpd/plugins /var/spool/torque /var/yp/Makefile" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.5/ext-active/ /etc/php/apache2-php5.6/ext-active/ /etc/php/cgi-php5.5/ext-active/ /etc/php/cgi-php5.6/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" DISTDIR="/usr/portage/distfiles" EMERGE_DEFAULT_OPTS="--nospinner --tree --quiet-build --deep --jobs 1" 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 userfetch userpriv usersandbox usersync" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://mirror.leaseweb.com/gentoo/ http://ftp.uni-erlangen.de/pub/mirrors/gentoo http://ftp-stud.hs-esslingen.de/pub/Mirrors/gentoo/ http://gd.tuwien.ac.at/opsys/linux/gentoo/" LANG="en_US.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j1" 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="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="" SYNC="rsync://rsync.de.gentoo.org/gentoo-portage" USE="acl amd64 berkdb bindist bzip2 cli cracklib crypt cxx dri fortran gdbm iconv ipv6 mbox mmx modules multilib ncurses nls nptl openmp pam pax_kernel pcre readline session sse sse2 ssl tcpd unicode 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="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" 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="fbdev glint intel mach64 mga nouveau nv r128 radeon savage sis tdfx trident vesa via vmware dummy v4l" 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, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
Created attachment 393268 [details] emerge log
Could you please report this upstream https://github.com/cole-trapnell-lab/cufflinks/issues
(In reply to Justin Lecher from comment #2) > Could you please report this upstream > > https://github.com/cole-trapnell-lab/cufflinks/issues done https://github.com/cole-trapnell-lab/cufflinks/issues/6
+ 08 Jan 2015; Justin Lecher <jlec@gentoo.org> cufflinks-1.3.0-r1.ebuild, + cufflinks-2.2.1.ebuild, cufflinks-2.2.1-r1.ebuild: + Add upper limit for boost dep as forced by upstream, #535716 +
commit bed71574b0b2911b0e667931508bb5b069883b64 Author: David Seifert <soap@gentoo.org> Date: Sun Apr 3 18:14:04 2016 +0200 sci-biology/cufflinks: Depend only on sci-biology/samtools:0.1-legacy Gentoo-Bug: 535716 * EAPI=6 * Updated boost in tree has fixed serialization for boost::shared_ptr * Build system is now orthogonal to sci-biology/samtools:0 and does not block updating to latest samtools
