Created attachment 303755 [details] the config.log I am unable to compile ccp4 because the dependency sci-chemistry/ccp4-apps-6.1.3-r10 can not be built. Steps to repeat: 1. emerge sci-chemistry/ccp4-apps-6.1.3-r10 The configuring the rapper section output is below: ********* RAPPER CONFIGURATION *********** Updating modification times for configuration files Please wait... ...done. configure --enable-shared=yes --exec_prefix=/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r10/work/ccp4-6.1.3 --prefix=/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r10/work/ccp4-6.1.3 --bindir=/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r10/work/ccp4-6.1.3/bin --libdir=/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r10/work/ccp4-6.1.3/lib --disable-shared checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make -j3 sets $(MAKE)... yes checking whether the C++ compiler works... no configure: error: in `/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r10/work/ccp4-6.1.3/src/rapper': configure: error: C++ compiler cannot create executables See `config.log' for more details Below is my emerge --info: Portage 2.1.10.44 (default/linux/amd64/10.0/desktop/kde, gcc-4.5.3, glibc-2.13-r4, 3.2.1-gentoo-r2 x86_64) ================================================================= System uname: Linux-3.2.1-gentoo-r2-x86_64-Intel-R-_Core-TM-2_Duo_CPU_E8400_@_3.00GHz-with-gentoo-2.0.3 Timestamp of tree: Tue, 28 Feb 2012 15:15:01 +0000 app-shells/bash: 4.1_p9 dev-java/java-config: 2.1.11-r3 dev-lang/python: 2.7.2-r3, 3.1.4-r3, 3.2.2 dev-util/cmake: 2.8.6-r4 dev-util/pkgconfig: 0.26 sys-apps/baselayout: 2.0.3 sys-apps/openrc: 0.9.8.4 sys-apps/sandbox: 2.5 sys-devel/autoconf: 2.13, 2.68 sys-devel/automake: 1.9.6-r3, 1.10.3, 1.11.1 sys-devel/binutils: 2.21.1-r1 sys-devel/gcc: 3.4.6-r2, 4.5.3-r2 sys-devel/gcc-config: 1.4.1-r1 sys-devel/libtool: 2.4-r1 sys-devel/make: 3.82-r1 sys-kernel/linux-headers: 3.1 (virtual/os-headers) sys-libs/glibc: 2.13-r4 Repositories: gentoo science ikelos ibormuth ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="* Intel-SDP" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=core2 -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /var/lib/hsqldb" 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-php5.3/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cli-php5.3/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" CXXFLAGS="-march=core2 -O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests binpkg-logs distlocks ebuild-locks fixlafiles news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch" FFLAGS="" GENTOO_MIRRORS="ftp://mirror.mcs.anl.gov/pub/gentoo/ ftp://ftp.ussg.iu.edu/pub/linux/gentoo http://gentoo.osuosl.org/" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="en" MAKEOPTS="-j3" 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="/var/lib/layman/science /var/lib/layman/ikelos /var/lib/layman/ibormuth" SYNC="rsync://rsync.us.gentoo.org/gentoo-portage" USE="R X a52 aac acl acpi aim airplay alsa amd64 apbs aspell balbes berkdb bluetooth boost branding bzip2 cairo cdda cdr cg cli color colors consolekit corefonts coverart cpudetection cracklib crypt css cuda cups cvs cxx dbus declarative dhcpcd dht double-precision dri dts dvd dvdr ebook eclipse embedded emboss encode excel exif faac fam fat fbsplash ffmpeg fftw firefox flac fontconfig fortran ftp fuse gd gdbm gdu gif gimp git gnuplot gnutella gpg gpm graphicsmagick gromacs gtk gui gzip hpcups hpijs http httpd icc iconv ifc imagemagick ipod ipv6 java jpeg jpeg2k kde kipi konqueror lame lastfm lastfmradio lcms ldap libkms libmpeg2 libnotify lzma mad matroska md5 md5sum mdadm mediaplayer memcache mjpeg mkl mmx mng modules mono motif mp3 mp4 mpeg mplayer mudflap multilib music musicbrainz ncurses net nfs nfsv4 nls nptl nptlonly nsplugin ntfs ntfsprogs ntp ntpd numpy nvidia ocaml octave ogg okular opencl opengl openmp openssl pam pango pcre pdf perl pgo phonon php plasma player plugins png policykit ppds pppd python qt3support qt4 rar raw readline samba science sdl semantic-desktop session sftp shaders smbclient smp solver sound speech speex spell sqlite sse sse2 sse3 ssh ssl ssse3 startup-notification stereo subversion sudo svg sysfs tcpd thumbnail thumbnails tiff timidity tk tools truetype tsmuxer udev unicode unzip upnp usb utils utp vcd vdpau video videos vim vim-syntax vlc vmd vnc vorbis vpx web webkit win32 x264 xcb xcomposite xinerama xml xorg xosd xscreensaver xulrunner xv xvfb xvid yahoo youtube zip zlib" 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" 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 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 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="evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en" PHP_TARGETS="php5-3" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nvidia" 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
Looks like make variables in a configure script. :)
Reproduced. Please attach build.log
which blas/lapck etc do you have installed?
Created attachment 303843 [details] build log
I am using sci-libs/blas-reference-20070226 sci-libs/lapack-reference 3.1.1-r1
Blocking x86 stabilization of this package because of this.
Reproduced using sci-libs/atlas-3.9.70 using both atlas and atlas-threaded profiles.
(In reply to comment #7) > Reproduced using sci-libs/atlas-3.9.70 using both atlas and atlas-threaded > profiles. Presumably most people who look at this bug are also science overlay users, so I think it's worth adding this comment. The reason I had to rebuild ccp4-apps is that /usr/lib64/libeigen_blas.so disappeared because dev-cpp/eigen:3::gentoo doens't install a library where eigen:3::science does. Ensuring that eigen:3::science gets installed is a workaround for me, although the ccp4-apps build still fails. dev-cpp/eigen is a dependency of virtual/blas-2.1::science.
I don't think this is an lapack/blas issue
Same on ~amd64, no science overlay. /usr/bin/uname -p = Intel(R) Core(TM)2 Quad CPU Q9550 @ 2.83GHz /bin/uname -X = unknown /bin/arch = unknown /usr/bin/arch -k = unknown /usr/convex/getsysinfo = unknown /usr/bin/hostinfo = unknown /bin/machine = unknown /usr/bin/oslevel = unknown /bin/universe = unknown configure:2746: checking whether make -j1 sets $(MAKE) configure:2768: result: yes configure:2960: checking for C++ compiler version configure:2969: x86_64-pc-linux-gnu-g++ --version >&5 x86_64-pc-linux-gnu-g++ (Gentoo 4.6.3 p1.0, pie-0.5.0) 4.6.3 Copyright (C) 2011 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. configure:2980: $? = 0 configure:2969: x86_64-pc-linux-gnu-g++ -v >&5 Using built-in specs. COLLECT_GCC=/usr/x86_64-pc-linux-gnu/gcc-bin/4.6.3/x86_64-pc-linux-gnu-g++ COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-pc-linux-gnu/4.6.3/lto-wrapper Target: x86_64-pc-linux-gnu Configured with: /var/tmp/portage/sys-devel/gcc-4.6.3/work/gcc-4.6.3/configure --prefix=/usr --bindir=/usr/x86_64-pc-linux-gnu/gcc-bin/4.6.3 --includedir=/usr/lib/gcc/x86_64-pc-linux-gnu/4.6.3/include --datadir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.6.3 --mandir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.6.3/man --infodir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.6.3/info --with-gxx-include-dir=/usr/lib/gcc/x86_64-pc-linux-gnu/4.6.3/include/g++-v4 --host=x86_64-pc-linux-gnu --build=x86_64-pc-linux-gnu --disable-altivec --disable-fixed-point --with-ppl --with-cloog --disable-ppl-version-check --with-cloog-include=/usr/include/cloog-ppl --enable-lto --enable-nls --without-included-gettext --with-system-zlib --disable-werror --enable-secureplt --enable-multilib --enable-libmudflap --disable-libssp --enable-libgomp --with-python-dir=/share/gcc-data/x86_64-pc-linux-gnu/4.6.3/python --enable-checking=release --enable-java-awt=gtk --enable-objc-gc --enable-languages=c,c++,java,go,objc,obj-c++,fortran --enable-shared --enable-threads=posix --enable-__cxa_atexit --enable-clocale=gnu --enable-targets=all --with-bugurl=http://bugs.gentoo.org/ --with-pkgversion='Gentoo 4.6.3 p1.0, pie-0.5.0' Thread model: posix gcc version 4.6.3 (Gentoo 4.6.3 p1.0, pie-0.5.0) configure:2980: $? = 0 configure:2969: x86_64-pc-linux-gnu-g++ -V >&5 x86_64-pc-linux-gnu-g++: error: unrecognized option '-V' x86_64-pc-linux-gnu-g++: fatal error: no input files compilation terminated. configure:2980: $? = 1 configure:2969: x86_64-pc-linux-gnu-g++ -qversion >&5 x86_64-pc-linux-gnu-g++: error: unrecognized option '-qversion' x86_64-pc-linux-gnu-g++: fatal error: no input files compilation terminated. configure:2980: $? = 1 configure:3000: checking whether the C++ compiler works configure:3022: x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=core2 -fPIC -lccp4f -lccp4c -lmmdb $(XCIF_LIB) $(XLAPACK_LIB) $(CXX_LIBS) $(XLDFLAGS) conftest.cpp >&5 x86_64-pc-linux-gnu-g++: error: $(XCIF_LIB): No such file or directory x86_64-pc-linux-gnu-g++: error: $(XLAPACK_LIB): No such file or directory x86_64-pc-linux-gnu-g++: error: $(CXX_LIBS): No such file or directory x86_64-pc-linux-gnu-g++: error: $(XLDFLAGS): No such file or directory configure:3026: $? = 1 configure:3064: result: no configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "rapper_ccp4" | #define PACKAGE_TARNAME "rapper_ccp4" | #define PACKAGE_VERSION "1.0" | #define PACKAGE_STRING "rapper_ccp4 1.0" | #define PACKAGE_BUGREPORT "ccp4@dl.ac.uk" | #define PACKAGE_URL "" | #define PACKAGE "rapper_ccp4" | #define VERSION "1.0" | /* end confdefs.h. */ | | int | main () | { | | ; | return 0; | } configure:3069: error: in `/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r10/work/ccp4-6.1.3/src/rapper': configure:3071: error: C++ compiler cannot create executables
Same here on amd64. I'm suffering this issue on two boxes. However, one of them succesfully compiled ccp4-apps-6.1.3-r10 on Jan. the 12th, 2012, just two months ago, but now it also fails when trying to re-emerge it. I suspect the culprit might be one of the toolchain updates since then (I use the stable branch).
I agree. I too had it compile fine in January, but after a update (general world update), it failed on me too.
If anybody could suggest me a real hint I will fix it straight away. I have no clue, but I think it is related to some quoting issue in the configure scripts. And they might have become a problem now due to some update, maybe toolchain related.
(In reply to comment #13) > If anybody could suggest me a real hint I will fix it straight away. This works for me(TM), as far as the configure sequence goes.... sed 's:\\$(XCIF_LIB):\${XCIF_LIB}:g' -i ${S}/configure || die "madsedfail" sed 's:\\$(XLAPACK_LIB):\${XLAPACK_LIB}:g' -i ${S}/configure || die "madsedfail" sed 's:\\$(CXX_LIBS):\${CXX_LIBS}:g' -i ${S}/configure || die "madsedfail" sed 's:\\$(XLDFLAGS):\${XLDFLAGS}:g' -i ${S}/configure || die "madsedfail" But "make" fails at a random stage with: make[3]: Leaving directory `/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r10/work/ccp4-6.1.3/src/rapper/LOOP' Making all in data eigdet.o: In function `det2_': eigdet.f:(.text+0x279): undefined reference to `cheevd_' eigdet.o: In function `uit_ver_': eigdet.f:(.text+0x370f): undefined reference to `cher_' collect2: ld returned 1 exit status make[1]: *** [crunch2] Error 1 make[1]: *** Waiting for unfinished jobs.... or: make[3]: Entering directory `/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r10/work/ccp4-6.1.3/src/clipper_progs/src' Making all in pirate eigdet.o: In function `det2_': eigdet.f:(.text+0x279): undefined reference to `cheevd_' eigdet.o: In function `uit_ver_': eigdet.f:(.text+0x370f): undefined reference to `cher_' collect2: ld returned 1 exit status make[1]: *** [crunch2] Error 1 make[1]: *** Waiting for unfinished jobs.... or: make[3]: Entering directory `/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r10/work/ccp4-6.1.3/src/clipper_progs/src' Making all in pirate eigdet.o: In function `det2_': eigdet.f:(.text+0x279): undefined reference to `cheevd_' eigdet.o: In function `uit_ver_': eigdet.f:(.text+0x370f): undefined reference to `cher_' collect2: ld returned 1 exit status make[1]: *** [crunch2] Error 1 make[1]: *** Waiting for unfinished jobs.... But honestly, i do not know how to fix det2 and uit_ver!?
(In reply to comment #14) > (In reply to comment #13) > > If anybody could suggest me a real hint I will fix it straight away. > > This works for me(TM), as far as the configure sequence goes.... > > sed 's:\\$(XCIF_LIB):\${XCIF_LIB}:g' -i ${S}/configure || die "madsedfail" > sed 's:\\$(XLAPACK_LIB):\${XLAPACK_LIB}:g' -i ${S}/configure || die > "madsedfail" > sed 's:\\$(CXX_LIBS):\${CXX_LIBS}:g' -i ${S}/configure || die "madsedfail" > sed 's:\\$(XLDFLAGS):\${XLDFLAGS}:g' -i ${S}/configure || die "madsedfail" > > If this really works, I owe you a sixer!
So the fix was not complete but inspires me for the right solution. + 03 Apr 2012; Justin Lecher <jlec@gentoo.org> ccp4-apps-6.1.3-r10.ebuild: + fix for some unknown issue resulting in #406337, thanks Andreas Schürch for + the initial idea of the fix +
