Created attachment 400278 [details] emerge log checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for gzread in -lz... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for memset... yes checking for strdup... yes checking for strrchr... yes checking for strtol... yes checking for strsep... yes checking host system type... x86_64-pc-linux-gnu checking how to create a pax tar archive... gnutar checking dependency style of x86_64-pc-linux-gnu-gcc... (cached) none checking dependency style of x86_64-pc-linux-gnu-g++... (cached) none checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating config.h config.status: executing depfiles commands -- tophat 2.0.9 Configuration Results -- C++ compiler: x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -DNDEBUG -pthread -I/usr/include -I/usr/include -I./SeqAn-1.3 Linker flags: -Wl,-O1 -Wl,--as-needed GCC version: x86_64-pc-linux-gnu-gcc (Gentoo Hardened 4.8.3 p1.1, pie-0.5.9) 4.8.3 Host System type: x86_64-pc-linux-gnu Install prefix: /usr Install eprefix: ${prefix} See config.h for further configuration information. Email <tophat.cufflinks@gmail.com> with questions and bug reports. >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/tophat-2.0.9/work/tophat-2.0.9 ... >>> Working in BUILD_DIR: "/var/tmp/portage/sci-biology/tophat-2.0.9/work/tophat-2.0.9_build" make -j1 make all-recursive make[1]: Entering directory '/var/tmp/portage/sci-biology/tophat-2.0.9/work/tophat-2.0.9_build' Making all in src make[2]: Entering directory '/var/tmp/portage/sci-biology/tophat-2.0.9/work/tophat-2.0.9_build/src' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-biology/tophat-2.0.9/work/tophat-2.0.9/src -I.. -march=native -O2 -pipe -DNDEBUG -pthread -I/usr/include -I/usr/include -I./SeqAn-1.3 -c -o reads.o /var/tmp/portage/sci-biology/tophat-2.0.9/work/tophat-2.0.9/src/reads.cpp /var/tmp/portage/sci-biology/tophat-2.0.9/work/tophat-2.0.9/src/reads.cpp:21:24: fatal error: seqan/find.h: No such file or directory #include <seqan/find.h> ^ compilation terminated. Makefile:1335: recipe for target 'reads.o' failed make[2]: *** [reads.o] Error 1 make[2]: Leaving directory '/var/tmp/portage/sci-biology/tophat-2.0.9/work/tophat-2.0.9_build/src' Makefile:392: recipe for target 'all-recursive' failed make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory '/var/tmp/portage/sci-biology/tophat-2.0.9/work/tophat-2.0.9_build' Makefile:333: recipe for target 'all' failed make: *** [all] Error 2 * ERROR: sci-biology/tophat-2.0.9::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/tophat-2.0.9::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/tophat-2.0.9::gentoo'`. * The complete build log is located at '/var/log/portage/sci-biology:tophat-2.0.9:20150330-180304.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/tophat-2.0.9/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/tophat-2.0.9/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/tophat-2.0.9/work/tophat-2.0.9_build' * S: '/var/tmp/portage/sci-biology/tophat-2.0.9/work/tophat-2.0.9' * GNU info directory index is up-to-date. quick search: https://bugs.gentoo.org/buglist.cgi?quicksearch=sci-biology%2Ftophat Portage 2.2.18 (python 2.7.9-final-0, hardened/linux/amd64, gcc-4.8.3, glibc-2.20-r2, 3.19.3-hardened x86_64) ================================================================= System uname: Linux-3.19.3-hardened-x86_64-Intel-R-_Core-TM-_i7-3770_CPU_@_3.40GHz-with-gentoo-2.2 KiB Mem: 16164756 total, 4968580 free KiB Swap: 16777212 total, 16726396 free Timestamp of repository gentoo: Mon, 30 Mar 2015 15:00:01 +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-lang/perl: 5.20.2::gentoo dev-lang/python: 2.7.9-r2::gentoo, 3.3.5-r1::gentoo dev-util/cmake: 3.1.0::gentoo dev-util/pkgconfig: 0.28-r2::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-r1::gentoo sys-devel/automake: 1.11.6-r1::gentoo, 1.12.6::gentoo, 1.13.4::gentoo, 1.14.1::gentoo, 1.15::gentoo sys-devel/binutils: 2.25::gentoo sys-devel/gcc: 4.8.3::gentoo, 4.9.2::gentoo sys-devel/gcc-config: 1.8::gentoo sys-devel/libtool: 2.4.6-r1::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: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc" 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" CXXFLAGS="-march=native -O2 -pipe" DISTDIR="/var/tmp/distfiles" EMERGE_DEFAULT_OPTS="--nospinner --tree --quiet-build --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 xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://ftp.uni-erlangen.de/pub/mirrors/gentoo rsync://mirror.netcologne.de/gentoo/ ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gor.bytemark.co.uk/gentoo/ rsync://ftp.snt.utwente.nl/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" USE="X acl aes-ni alsa amd64 apache2 avx avx2 berkdb bzip2 cairo cli corefonts cracklib crypt cups cxx dbus dnssec dot dri drmkms dvd ecc extraengine ffmpeg fontconfig fortran fpm gd gdbm gif gtk gudev gui hardened iconv icu isag jadetex jpeg justify kvm lapack libav libkms libvirtd logrotate mbox minizip mmx mmxext modules multilib mysql ncurses nls nptl ogg opengl openmp openssl pam pax_kernel pcre pcre16 plasma png policykit python qemu qt3support readline sdl session spice sqlite sse sse2 sse4 sse4_1 sse4_2 ssh-askpass ssl ssse3 svg tcpd theora thinkpad threads tk tls truetype uml unicode urandom usb usbredir uxa v4l v4l2 video vorbis xa xattr xkb xmp xscreensaver xslt xtpax xvfb xvmc zenmap 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" 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-conso le presenter-minimizer" LINGUAS="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="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
Same here. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/mnt/1TB/var/tmp/portage/sci-biology/tophat-2.0.9/work/tophat-2.0.9/src -I.. -O2 -pipe -maes -mpclmul -mpopcnt -mavx -march=native -DNDEBUG -pthread -I/usr/include -I/usr/include -I./SeqAn-1.3 -c -o bwt_map.o /mnt/1TB/var/tmp/portage/sci-biology/tophat-2.0.9/work/tophat-2.0.9/src/bwt_map.cpp /mnt/1TB/var/tmp/portage/sci-biology/tophat-2.0.9/work/tophat-2.0.9/src/reads.cpp:21:24: fatal error: seqan/find.h: No such file or directory #include <seqan/find.h> ^ compilation terminated. Makefile:1335: recipe for target 'reads.o' failed make[2]: *** [reads.o] Error 1 make[2]: *** Waiting for unfinished jobs.... /mnt/1TB/var/tmp/portage/sci-biology/tophat-2.0.9/work/tophat-2.0.9/src/bwt_map.cpp:21:28: fatal error: seqan/sequence.h: No such file or directory #include <seqan/sequence.h> ^ compilation terminated. Makefile:1335: recipe for target 'bwt_map.o' failed make[2]: *** [bwt_map.o] Error 1 make[2]: Leaving directory '/mnt/1TB/var/tmp/portage/sci-biology/tophat-2.0.9/work/tophat-2.0.9_build/src' Further, I think configure should be passed with '--enable-intel64' for amd64: --enable-intel64 optimize for Intel64 CPU such as Xeon and Core2
(In reply to Martin Mokrejš from comment #1) > reads.cpp:21:24: fatal error: seqan/find.h: No such file or directory > #include <seqan/find.h> > bwt_map.cpp:21:28: fatal error: seqan/sequence.h: No such file or directory > #include <seqan/sequence.h> Forgot to add I have seqan-2.0.0 and it installed only /usr/bin/ and /usr/share contents.
(In reply to Martin Mokrejš from comment #2) > (In reply to Martin Mokrejš from comment #1) > > > reads.cpp:21:24: fatal error: seqan/find.h: No such file or directory > > #include <seqan/find.h> > > > bwt_map.cpp:21:28: fatal error: seqan/sequence.h: No such file or directory > > #include <seqan/sequence.h> > > > Forgot to add I have seqan-2.0.0 and it installed only /usr/bin/ and > /usr/share contents. That's the problem, there is no lib anymore and thus no header. seqan-1.3.1-r1 works, but that doesn't compile on modern compilers and I have no clue how to fix that.
Just opened https://github.com/seqan/seqan/issues/954
Created attachment 401382 [details] seqan-2.0.0-r1.ebuild Ugly but works. See also https://github.com/seqan/seqan/issues/954
(In reply to Martin Mokrejš from comment #5) > Created attachment 401382 [details] > seqan-2.0.0-r1.ebuild > > Ugly but works. > > See also https://github.com/seqan/seqan/issues/954 Sorry, I attached it to a wrong bug. ;-) But won't create yet another for seqan-2.0.0.
(In reply to Martin Mokrejš from comment #6) > (In reply to Martin Mokrejš from comment #5) > > Created attachment 401382 [details] > > seqan-2.0.0-r1.ebuild > > > > Ugly but works. > > > > See also https://github.com/seqan/seqan/issues/954 > > Sorry, I attached it to a wrong bug. ;-) But won't create yet another for > seqan-2.0.0. Thank you very much for following this up. I will look into that.
commit 3bae7944956edffc244eb7d8e55bc0c786013ed0 Author: David Seifert <soap@gentoo.org> Date: Sat Apr 9 20:37:04 2016 +0200 sci-biology/tophat: Version bump, use samtools:0.1-legacy Gentoo-Bug: 545154, 546816, 566494, 572054 * EAPI=6 * Unbundle samtools and SeqAn * Fix broken shebangs in python scripts
