Hi, this is likely a gcc-6.4.0-related issue when I need to recompile all apps. Previously I installed this using gcc-4.9.4. >>> Emerging (1 of 2) dev-haskell/samtools-0.2.4.3::haskell * samtools-0.2.4.3.tar.gz BLAKE2B SHA512 size ;-) ... [ ok ] >>> Unpacking source... >>> Unpacking samtools-0.2.4.3.tar.gz to /scratch/var/tmp/portage/dev-haskell/samtools-0.2.4.3/work >>> Source unpacked in /scratch/var/tmp/portage/dev-haskell/samtools-0.2.4.3/work >>> Preparing source in /scratch/var/tmp/portage/dev-haskell/samtools-0.2.4.3/work/samtools-0.2.4.3 ... >>> Source prepared. >>> Configuring source in /scratch/var/tmp/portage/dev-haskell/samtools-0.2.4.3/work/samtools-0.2.4.3 ... * Using cabal-1.24.2.0. * Prepending /usr/lib64/ghc-8.0.2 to LD_LIBRARY_PATH /usr/bin/ghc -package Cabal-1.24.2.0 --make /scratch/var/tmp/portage/dev-haskell/samtools-0.2.4.3/work/samtools-0.2.4.3/Setup.hs -j2 +RTS -A256M -qb0 -RTS -threaded -dynamic -o setup [1 of 1] Compiling Main ( /scratch/var/tmp/portage/dev-haskell/samtools-0.2.4.3/work/samtools-0.2.4.3/Setup.hs, /scratch/var/tmp/portage/dev-haskell/samtools-0.2.4.3/work/samtools-0.2.4.3/Setup.o ) Linking setup ... ./setup configure --ghc --prefix=/usr --with-compiler=/usr/bin/ghc --with-hc-pkg=/usr/bin/ghc-pkg --prefix=/usr --libdir=/usr/lib64 --libsubdir=samtools-0.2.4.3/ghc-8.0.2 --datadir=/usr/share/ --datasubdir=samtools-0.2.4.3/ghc-8.0.2 --ghc-options=-j2 +RTS -A256M -qb0 -RTS --with-ar=x86_64-pc-linux-gnu-ar --ghc-option=-optc-O2 --ghc-option=-optc-pipe --ghc-option=-optc-mpclmul --ghc-option=-optc-mpopcnt --ghc-option=-optc-march=native --ghc-option=-optc-ftree-vectorize --ghc-option=-optl-Wl,-O1 --ghc-option=-optl-Wl,--as-needed --disable-executable-stripping --docdir=/usr/share/doc/samtools-0.2.4.3 --verbose --enable-shared --enable-executable-dynamic --sysconfdir=/etc --disable-library-stripping --flag=-tests Configuring samtools-0.2.4.3... Flags chosen: tests=False Dependency base >=4.5 && <5: using base-4.9.1.0 Dependency bytestring -any: using bytestring-0.10.8.1 Dependency seqloc >=0.3.1: using seqloc-0.6.1.1 Dependency vector >=0.7: using vector-0.11.0.0 Using Cabal-1.24.2.0 compiled by ghc-8.0 Using compiler: ghc-8.0.2 Using install prefix: /usr Binaries installed in: /usr/bin Libraries installed in: /usr/lib64/samtools-0.2.4.3/ghc-8.0.2 Dynamic libraries installed in: /usr/lib64/x86_64-linux-ghc-8.0.2 Private binaries installed in: /usr/libexec Data files installed in: /usr/share/samtools-0.2.4.3/ghc-8.0.2 Documentation installed in: /usr/share/doc/samtools-0.2.4.3 Configuration files installed in: /etc Using alex version 3.2.3 found on system at: /usr/bin/alex Using ar given by user at: /usr/bin/x86_64-pc-linux-gnu-ar Using c2hs version 0.28.3 found on system at: /usr/bin/c2hs Using cpphs version 1.20.8 found on system at: /usr/bin/cpphs Using gcc version 6.3.0 found on system at: /usr/bin/x86_64-pc-linux-gnu-gcc Using ghc version 8.0.2 given by user at: /usr/bin/ghc Using ghc-pkg version 8.0.2 given by user at: /usr/bin/ghc-pkg No ghcjs found No ghcjs-pkg found No greencard found Using haddock version 2.17.3 found on system at: /usr/bin/haddock-ghc-8.0.2 Using happy version 1.19.8 found on system at: /usr/bin/happy Using haskell-suite found on system at: haskell-suite-dummy-location Using haskell-suite-pkg found on system at: haskell-suite-pkg-dummy-location No hmake found Using hpc version 0.67 found on system at: /usr/bin/hpc Using hsc2hs version 0.68.1 found on system at: /usr/bin/hsc2hs No hscolour found No jhc found Using ld found on system at: /usr/bin/x86_64-pc-linux-gnu-ld No lhc found No lhc-pkg found Using pkg-config version 0.29.2 found on system at: /usr/bin/pkg-config Using strip version 2.29 found on system at: /usr/bin/strip Using tar found on system at: /bin/tar No uhc found >>> Source configured. >>> Compiling source in /scratch/var/tmp/portage/dev-haskell/samtools-0.2.4.3/work/samtools-0.2.4.3 ... ./setup build Building samtools-0.2.4.3... Preprocessing library samtools-0.2.4.3... c2hs: C header contains errors: /usr/include/bits/floatn.h:73: (column 29) [ERROR] >>> Syntax error ! The symbol `;' does not fit here. * ERROR: dev-haskell/samtools-0.2.4.3::haskell failed (compile phase): * setup build failed * * Call stack: * ebuild.sh, line 124: Called src_compile * environment, line 2822: Called haskell-cabal_src_compile * environment, line 2020: Called cabal_src_compile * environment, line 736: Called cabal-build * environment, line 496: Called die * The specific snippet of code: * ./setup "$@" || die "setup build failed" * * If you need support, post the output of `emerge --info '=dev-haskell/samtools-0.2.4.3::haskell'`, * the complete build log and the output of `emerge -pqv '=dev-haskell/samtools-0.2.4.3::haskell'`. * The complete build log is located at '/scratch/var/tmp/portage/dev-haskell/samtools-0.2.4.3/temp/build.log'. * The ebuild environment file is located at '/scratch/var/tmp/portage/dev-haskell/samtools-0.2.4.3/temp/environment'. * Working directory: '/scratch/var/tmp/portage/dev-haskell/samtools-0.2.4.3/work/samtools-0.2.4.3' * S: '/scratch/var/tmp/portage/dev-haskell/samtools-0.2.4.3/work/samtools-0.2.4.3' # emerge --info '=dev-haskell/samtools-0.2.4.3::haskell' Portage 2.3.19 (python 2.7.14-final-0, default/linux/amd64/17.0, gcc-6.3.0, glibc-2.26-r5, 4.14.14-default-pciehp x86_64) ================================================================= System Settings ================================================================= System uname: Linux-4.14.14-default-pciehp-x86_64-Intel-R-_Core-TM-_i7-2640M_CPU_@_2.80GHz-with-gentoo-2.4.1 KiB Mem: 16366712 total, 9818448 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Wed, 24 Jan 2018 08:30:01 +0000 Head commit of repository gentoo: a74882310cce93d47ec2c011bab114a8ab8679db sh bash 4.4_p12-r1 ld GNU ld (Gentoo 2.29.1 p3) 2.29.1 app-shells/bash: 4.4_p12-r1::gentoo dev-java/java-config: 2.2.0-r3::gentoo dev-lang/perl: 5.26.9999::gentoo dev-lang/python: 2.7.14-r1::gentoo, 3.4.6-r1::gentoo, 3.5.4-r1::gentoo, 3.6.4::gentoo dev-util/cmake: 3.10.2::gentoo dev-util/pkgconfig: 0.29.2::gentoo sys-apps/baselayout: 2.4.1-r2::gentoo sys-apps/openrc: 0.34.11::gentoo sys-apps/sandbox: 2.12::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69-r4::gentoo sys-devel/automake: 1.11.6-r2::gentoo, 1.12.6-r1::gentoo, 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15.1-r1::gentoo sys-devel/binutils: 2.29.1-r1::gentoo sys-devel/gcc: 4.3.6-r1::gentoo, 4.4.7::gentoo, 4.6.4::gentoo, 4.7.4::gentoo, 4.8.5::gentoo, 4.9.4::gentoo, 5.3.0::gentoo, 5.4.0-r3::gentoo, 6.2.0-r1::gentoo, 6.3.0::gentoo, 7.1.0-r1::gentoo, 7.2.0-r1::gentoo sys-devel/gcc-config: 1.9.1::gentoo sys-devel/libtool: 2.4.6-r4::gentoo sys-devel/make: 4.2.1-r1::gentoo sys-kernel/linux-headers: 4.14::gentoo (virtual/os-headers) sys-libs/glibc: 2.26-r5::gentoo Repositories: gentoo location: /scratch/usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sync-rsync-extra-opts: science location: /scratch/mmokrejs/proj/sci masters: gentoo priority: 0 layman location: /var/lib/layman masters: gentoo priority: 1 haskell location: /var/lib/layman/haskell masters: gentoo priority: 50 vmware location: /var/lib/layman/vmware masters: gentoo priority: 50 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 OPERA-2014 RAR Intel-SDP" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /etc/stunnel/stunnel.conf /usr/lib64/libreoffice/program/sofficerc /usr/share/easy-rsa /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.2/conf /usr/share/maven-bin-3.3/conf /var/bind /var/lib/hsqldb /var/spool/torque" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.6/ext-active/ /etc/php/apache2-php7.1/ext-active/ /etc/php/cgi-php5.6/ext-active/ /etc/php/cgi-php7.1/ext-active/ /etc/php/cli-php5.6/ext-active/ /etc/php/cli-php7.1/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 -mpclmul -mpopcnt -march=native -ftree-vectorize" DISTDIR="/scratch/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync multilib-strict news nostrip parallel-fetch preserve-libs protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://gentoo.wheel.sk/ http://ftp.fi.muni.cz/pub/linux/gentoo/ http://gentoo.mirror.web4u.cz/ rsync://gentoo.mirror.dkm.cz/gentoo/ ftp://gentoo.mirror.web4u.cz/" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="en_US en_GB en cs" 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 --exclude=/.git" PORTAGE_TMPDIR="/scratch/var/tmp" USE="R X acpi alsa amd64 amr apache apache2 asm avx berkdb bluetooth boost bzip2 cairo cgi cli coin consolekit cracklib crypt cryptlib cryptsetup cups cxx dbus device-mapper dhcp directfb dri drm dvd emboss encode fax fbcon ffmpeg flac fontconfig fortran fuse gbm gcrypt gd gdbm geoip geolocation gimp glpk gmp gnutls gpm gps gtk hal hpijs hwdb iconv id3tag imaging innodb inotify java javafx javascript jce jpeg jpg js jscript keymap ladspa lame lapack laptop lcms libnotify lm_sensors mad matroska mmx modemmanager modules mp3 multicore multilib multimedia mysql ncurses networkmanager nfs nls nptl nptlonly nscd ntfs ntfsdecrypt ntfsprogs objc ocr ogg opengl openmp pam parport pcre pcre16 pdf pdfimport pdl perl php pkcs11 plplot png policykit polkit postproc postscript ppds ppp pppd pptx pulseaudio python qt3support qt4 qt5 readline rendering resolvconf samba scanner sctp seccomp server session sha512 slideshow sna sndfile sqlite sse sse2 sse3 sse4_1 sse4_2 ssh ssh-agent ssl sslv2 sslv3 ssse3 startup-notification suexec svg syslog tcl tcpd threads tiff tk truetype twolame udev unicode upower usb v4l v4l2 vim-syntax vnc wavpack wifi x11 xattr xcb xml xorg xrandr xv xvid xvmc zlib" ABI_X86="64 32" 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" 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="aivdm ashtech earthmate evermore fv18 garmin garmintxt gpsclock isync itrax mtk3301 navcom ntrip oceanserver oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 tnt tripmate tsip ublox fury geostar nmea0183 nmea2000 passthrough" GRUB_PLATFORMS="pc" INPUT_DEVICES="libinput keyboard mouse" KERNEL="linux" L10N="en-US en en-GB cs" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" POSTGRES_TARGETS="postgres9_5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_5" RUBY_TARGETS="ruby20 ruby21 ruby23 ruby24 ruby25" USERLAND="GNU" VIDEO_CARDS="vesa vmware fbdev intel i915 i965" 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: CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS ================================================================= Package Settings ================================================================= dev-haskell/samtools-0.2.4.3::haskell was built with the following: USE="-doc -hoogle -hscolour -profile" ABI_X86="(64)"
*** This bug has been marked as a duplicate of bug 644200 ***
Created attachment 517010 [details] build.log HCFLAGS=-v emerge -1 dev-haskell/samtools
