sci-libs/umfpack-5.5.1 fail to emerge on two amd64 machines: a HP ProLiant ML150 G6 and Mackbook Pro 6.1. Both machines are up-to-date (eix-sync, emerge -uND world, emerge --depclean, revdep-rebuild etc.) I have FFLAGS="${CFLAGS} -fdefault-integer-8" FCFLAGS="${CFLAGS} -fdefault-integer-8" in /etc/make.conf (64-bit int support Octave ind its deps.) Note: sci-libs/umfpack-5.5.1 does, however, build on two other machines I have. Reproducible: Always Steps to Reproduce: 1.EXTRA_ECONF="--with-blas=/usr/local/lib/libBLAS.so" emerge umfpack (emerge umfpack fails too) 2. 3. Actual Results: # EXTRA_ECONF="--with-blas=/usr/local/lib/libBLAS.so" emerge umfpack * IMPORTANT: 5 news items need reading for repository 'gentoo'. * Use eselect news to read news items. Calculating dependencies... done! >>> Verifying ebuild manifests >>> Emerging (1 of 1) sci-libs/umfpack-5.5.1 * UMFPACK-5.5.1.tar.gz RMD160 SHA1 SHA256 size ;-) ... [ ok ] * Package: sci-libs/umfpack-5.5.1 * Repository: gentoo * Maintainer: sci@gentoo.org * USE: amd64 elibc_glibc kernel_linux metis multilib userland_GNU * FEATURES: sandbox >>> Unpacking source... >>> Unpacking UMFPACK-5.5.1.tar.gz to /var/tmp/portage/sci-libs/umfpack-5.5.1/work >>> Source unpacked in /var/tmp/portage/sci-libs/umfpack-5.5.1/work >>> Preparing source in /var/tmp/portage/sci-libs/umfpack-5.5.1/work/UMFPACK ... * Applying umfpack-5.5.0-autotools.patch ... [ ok ] * Running eautoreconf in '/var/tmp/portage/sci-libs/umfpack-5.5.1/work/UMFPACK' ... * Running aclocal ... [ ok ] * Running libtoolize --copy --force --install --automake ... [ ok ] * Running aclocal ... [ ok ] * Running autoconf ... [ ok ] * Running automake --add-missing --copy --foreign ... [ ok ] * Running elibtoolize in: UMFPACK/ * Applying portage-2.2.patch ... * Applying sed-1.5.6.patch ... * Applying as-needed-2.2.6.patch ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-libs/umfpack-5.5.1/work/UMFPACK ... * econf: updating UMFPACK/config.guess with /usr/share/gnuconfig/config.guess * econf: updating UMFPACK/config.sub with /usr/share/gnuconfig/config.sub ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --libdir=/usr/lib64 --with-blas=-lblas --disable-static --with-cholmod --with-blas=/usr/local/lib/libBLAS.so 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 sets $(MAKE)... yes checking for x86_64-pc-linux-gnu-g77... no checking for x86_64-pc-linux-gnu-xlf... no checking for x86_64-pc-linux-gnu-f77... no checking for x86_64-pc-linux-gnu-frt... no checking for x86_64-pc-linux-gnu-pgf77... no checking for x86_64-pc-linux-gnu-cf77... no checking for x86_64-pc-linux-gnu-fort77... no checking for x86_64-pc-linux-gnu-fl32... no checking for x86_64-pc-linux-gnu-af77... no checking for x86_64-pc-linux-gnu-xlf90... no checking for x86_64-pc-linux-gnu-f90... no checking for x86_64-pc-linux-gnu-pgf90... no checking for x86_64-pc-linux-gnu-pghpf... no checking for x86_64-pc-linux-gnu-epcf90... no checking for x86_64-pc-linux-gnu-gfortran... x86_64-pc-linux-gnu-gfortran checking whether the Fortran 77 compiler works... yes checking for Fortran 77 compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU Fortran 77 compiler... yes checking whether x86_64-pc-linux-gnu-gfortran accepts -g... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for style of include used by make... GNU checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc checking whether we are using the GNU C compiler... yes checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed checking dependency style of x86_64-pc-linux-gnu-gcc... gcc3 checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by x86_64-pc-linux-gnu-gcc... /usr/x86_64-pc-linux-gnu/bin/ld checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r checking for x86_64-pc-linux-gnu-objdump... x86_64-pc-linux-gnu-objdump checking how to recognize dependent libraries... pass_all checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib checking command to parse /usr/bin/nm -B output from x86_64-pc-linux-gnu-gcc object... ok checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if x86_64-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no checking for x86_64-pc-linux-gnu-gcc option to produce PIC... -fPIC -DPIC checking if x86_64-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes checking if x86_64-pc-linux-gnu-gcc static flag -static works... yes checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... yes checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... (cached) yes checking whether the x86_64-pc-linux-gnu-gcc linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking for x86_64-pc-linux-gnu-gfortran option to produce PIC... -fPIC checking if x86_64-pc-linux-gnu-gfortran PIC flag -fPIC works... yes checking if x86_64-pc-linux-gnu-gfortran static flag -static works... yes checking if x86_64-pc-linux-gnu-gfortran supports -c -o file.o... yes checking if x86_64-pc-linux-gnu-gfortran supports -c -o file.o... (cached) yes checking whether the x86_64-pc-linux-gnu-gfortran linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for sqrt in -lm... yes checking how to get verbose linking output from x86_64-pc-linux-gnu-gfortran... -v checking for Fortran 77 libraries of x86_64-pc-linux-gnu-gfortran... -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.5 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.5/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.5/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.5/../../.. -lgfortranbegin -lgfortran -lm checking for dummy main to link with Fortran 77 libraries... none checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore checking for sgemm_ in /usr/local/lib/libBLAS.so... yes checking for amd_aat in -lamd... yes checking cholmod.h usability... yes checking cholmod.h presence... yes checking for cholmod.h... yes checking for cholmod_solve in -lcholmod... no configure: error: Cannot find libcholmod !!! Please attach the following file when seeking support: !!! /var/tmp/portage/sci-libs/umfpack-5.5.1/work/UMFPACK/config.log * ERROR: sci-libs/umfpack-5.5.1 failed (configure phase): * econf failed * * Call stack: * ebuild.sh, line 56: Called src_configure * environment, line 2711: Called econf '--with-blas=-lblas ' '--disable-static' '--with-cholmod' * ebuild.sh, line 557: Called die * The specific snippet of code: * die "econf failed" * * If you need support, post the output of 'emerge --info =sci-libs/umfpack-5.5.1', * the complete build log and the output of 'emerge -pqv =sci-libs/umfpack-5.5.1'. * The complete build log is located at '/var/tmp/portage/sci-libs/umfpack-5.5.1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-libs/umfpack-5.5.1/temp/environment'. * S: '/var/tmp/portage/sci-libs/umfpack-5.5.1/work/UMFPACK' >>> Failed to emerge sci-libs/umfpack-5.5.1, Log file: >>> '/var/tmp/portage/sci-libs/umfpack-5.5.1/temp/build.log' * Messages for package sci-libs/umfpack-5.5.1: * ERROR: sci-libs/umfpack-5.5.1 failed (configure phase): * econf failed * * Call stack: * ebuild.sh, line 56: Called src_configure * environment, line 2711: Called econf '--with-blas=-lblas ' '--disable-static' '--with-cholmod' * ebuild.sh, line 557: Called die * The specific snippet of code: * die "econf failed" * * If you need support, post the output of 'emerge --info =sci-libs/umfpack-5.5.1', * the complete build log and the output of 'emerge -pqv =sci-libs/umfpack-5.5.1'. * The complete build log is located at '/var/tmp/portage/sci-libs/umfpack-5.5.1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-libs/umfpack-5.5.1/temp/environment'. * S: '/var/tmp/portage/sci-libs/umfpack-5.5.1/work/UMFPACK' * IMPORTANT: 5 news items need reading for repository 'gentoo'. * Use eselect news to read news items. emerge --info Portage 2.1.9.42 (default/linux/amd64/10.0, gcc-4.4.5, glibc-2.13-r2, 2.6.36-gentoo-r5 x86_64) ================================================================= System uname: Linux-2.6.36-gentoo-r5-x86_64-Intel-R-_Xeon-R-_CPU_E5504_@_2.00GHz-with-gentoo-1.12.14 Timestamp of tree: Wed, 30 Mar 2011 07:30:01 +0000 app-shells/bash: 4.1_p9 dev-java/java-config: 2.1.11-r3 dev-lang/python: 2.7.1-r1, 3.1.3-r1 dev-util/cmake: 2.8.4 sys-apps/baselayout: 1.12.14-r1 sys-apps/sandbox: 2.4 sys-devel/autoconf: 2.13, 2.65-r1 sys-devel/automake: 1.9.6-r3, 1.11.1 sys-devel/binutils: 2.21 sys-devel/gcc: 4.4.5, 4.5.2 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.10 sys-devel/make: 3.81-r2 virtual/os-headers: 2.6.36.1 (sys-kernel/linux-headers) ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=native --param l2-cache-size=512" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /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 -march=native --param l2-cache-size=512" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests binpkg-logs distlocks fixlafiles fixpackages news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch" FFLAGS="-O2 -pipe -march=native --param l2-cache-size=512 -fdefault-integer-8" GENTOO_MIRRORS="http://mirror.gentoo.no/" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j7" 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" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X acl amd64 berkdb bzip2 cli cracklib crypt cups cxx dri fortran gdbm gpm iconv ipv6 mmx modules mudflap multilib ncurses nls nptl nptlonly openmp pam pcre perl pppd python readline session sse sse2 ssl ssse3 svg sysfs tcpd unicode xorg 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" 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="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" PHP_TARGETS="php5-3" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nvidia 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, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LINGUAS, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY
...and what's the error in config.log ? Also, I kinda doubt that EXTRA_ECONF="--with-blas=/usr/local/lib/libBLAS.so" counts as a supported configuration.
Thanks Rafał. Looking in the /var/tmp/portage/sci-libs/umfpack-5.5.1/work/UMFPACK/config.log file solved it. Apperently one need to have LDFLAGS=-lgfortran when using the Goto BLAS lib (which I use) otherwise one gets <snip> configure:15116: result: yes configure:15116: checking for cholmod.h configure:15116: result: yes configure:15126: checking for cholmod_solve in -lcholmod configure:15159: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -march=native --param l2-cache-size=512 -Wl,-O1 -Wl,--as-needed conftest.c -lcholmod -lamd -lm >&5 /usr/local/lib/libBLAS.so: undefined reference to `_gfortran_concat_string' /usr/local/lib/libBLAS.so: undefined reference to `_gfortran_compare_string' /usr/local/lib/libBLAS.so: undefined reference to `_gfortran_pow_i8_i8' /usr/local/lib/libBLAS.so: undefined reference to `_gfortran_pow_r8_i8' /usr/local/lib/libBLAS.so: undefined reference to `_gfortran_pow_r4_i8' collect2: ld returned 1 exit status configure:15159: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "umfpack" | #define PACKAGE_TARNAME "umfpack" <snip> So emerging with: LDFLAGS=-lgfortran EXTRA_ECONF="--with-blas=-lBLAS" emerge umfpack works (where libBLAS.so -> libgoto2_nehalemp-r1.13.so)
If `equery belongs /usr/local/lib/libBLAS.so' returns a CATEGORY/PKG, then please reopen this bug report, because nothing we support should install to /usr/local/. If not, then consider that we cannot support anything installed /usr/local/ outside of the portage build / package management system.
