When emerging Octave 3.2.0, the configure script fails with the following error: ... checking for short... yes checking size of short... configure: error: cannot compute sizeof (short) See `config.log' for more details. !!! Please attach the following file when seeking support: !!! /var/tmp/portage/sci-mathematics/octave-3.2.0/work/octave-3.2.0/config.log * * ERROR: sci-mathematics/octave-3.2.0 failed. * Call stack: * ebuild.sh, line 49: Called src_configure * environment, line 3210: Called _eapi2_src_configure * ebuild.sh, line 628: Called econf * ebuild.sh, line 534: Called die * The specific snippet of code: * die "econf failed" * The die message: * econf failed * Please note that the most natural thing to try is `emerge -1 system`, but rebuilding these packages didn't fix the problem. Below is the output of `emerge --info`, and attached is the config.log (gzip compressed) produced by the configure script. Reproducible: Always Steps to Reproduce: 1. emerge =octave-3.2.0 2. 3.
Created attachment 197464 [details] Here is the config.log.gz
emerge --info Portage 2.1.6.13 (default/linux/amd64/2008.0, gcc-4.1.2, glibc-2.9_p20081201-r2, 2.6.20-gentoo-r8 x86_64) ================================================================= System uname: Linux-2.6.20-gentoo-r8-x86_64-Dual_Core_AMD_Opteron-tm-_Processor_280-with-glibc2.2.5 Timestamp of tree: Thu, 09 Jul 2009 20:00:19 +0000 app-shells/bash: 3.2_p39 dev-lang/python: 2.4.6, 2.5.4-r2 dev-python/pycrypto: 2.0.1-r6 sys-apps/baselayout: 1.12.11.1 sys-apps/sandbox: 1.6-r2 sys-devel/autoconf: 2.13, 2.63 sys-devel/automake: 1.4_p6, 1.5, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.2 sys-devel/binutils: 2.19.1-r1 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 1.5.26 virtual/os-headers: 2.6.27-r2 ACCEPT_KEYWORDS="amd64" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=opteron -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/X11/xkb" CONFIG_PROTECT_MASK="/etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/web2c /etc/udev/rules.d" CXXFLAGS="-march=opteron -O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="distlocks fixpackages parallel-fetch protect-owned sandbox sfperms strict unmerge-orphans userfetch" GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo" LDFLAGS="-Wl,-O1" MAKEOPTS="-j5" 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="/usr/portage/local/layman/science" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X acl amd64 berkdb blas bzip2 cli cracklib crypt cups dri firefox fortran gdbm gnome gpm gtk iconv ipv6 isdnlog midi mmx mudflap multilib ncurses nls nptl nptlonly openmp pam pcre perl pppd python readline reflection session spl sse sse2 ssl 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 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" ELIBC="glibc" INPUT_DEVICES="keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" USERLAND="GNU" VIDEO_CARDS="nv nvidia vesa"
As the error suggests: /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libblas.so: undefined reference to `_gfortran_runtime_error' problem seems to lie in libblas. Check for libblas succeeds, cause those fortran libs are added in the check, but later, there's no cleanup, so during that sizeof check libblas is still among libs, but the fortran libs no longer are. It's hard to tell, whether it's a failure on octave or libblas side.
rebuilding blas didn't seem to help.
Sorry for commenting without actually having tested or checked anything (I have no blas compiled, and have no time to compile it now). (In reply to comment #3) > Check for libblas succeeds, cause those fortran libs are added in the check [...] > It's hard to tell, whether it's a failure on octave or libblas side. This seems to be also an issue caused by the forced -Wl,--as-needed. As a temporary workaround, you might try to add --no-as-needed to your CFLAGS/CXXFLAGS/FFLAGS, but even if this should work this is only a hack. The real problem is (if your description is correct which I did not check) that libblas is not linked against all the libraries it uses, i.e. it is a bug of libblas which should have been linked with -lgfortran (or whatever the missing library is). Probably "-lgfortran" is missing somewhere in the libblas build system (probably in LIBS, but I have not checked).
Hi Troy, What blas implementation are you using? Thanks, Markus
Markus, Thanks for the reply. In fact I checked the BLAS with eselect and it was set to goto-blas. When I changed this to atlas-threads, Octave compiled just fine. Previous verstions (even >= 3.0) compiled just fine with goto-blas. Troy
Hi Troy, Is it ok if we close this bug since it seems to compile now. The error you were getting seemed to be more related to goto-blas than octave itself but I haven't investigated this any further. Thanks, Markus
That's fine. Thanks.
Great, thanks! Closing this one. cheers, Markus
