/usr/bin/gfortran -Wall -Wl,-O1 -shared build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/build/src.linux-x86_64-2.6/scipy/linalg/iterative/_iterativemodule.o build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/fortranobject.o build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/scipy/linalg/iterative/STOPTEST2.o build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/scipy/linalg/iterative/getbreak.o build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/scipy/linalg/iterative/BiCGREVCOM.o build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/scipy/linalg/iterative/BiCGSTABREVCOM.o build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/scipy/linalg/iterative/CGREVCOM.o build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/scipy/linalg/iterative/CGSREVCOM.o build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/scipy/linalg/iterative/GMRESREVCOM.o build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/scipy/linalg/iterative/QMRREVCOM.o -L/usr/lib64 -L/usr/lib64 -Lbuild/temp.linux-x86_64-2.6 -llapack -lblas -lcblas -latlas -lcblas -latlas -lpython2.6 -lgfortran -o build/lib.linux-x86_64-2.6/scipy/linalg/_iterative.so building 'scipy.linsolve._zsuperlu' extension compiling C sources C compiler: x86_64-pc-linux-gnu-gcc -pthread -fno-strict-aliasing -march=nocona -O2 -pipe -fPIC compile options: '-DATLAS_INFO="\"3.9.3\"" -DUSE_VENDOR_BLAS=1 -I/usr/lib64/python2.6/site-packages/numpy/core/include -I/usr/include/python2.6 -c' x86_64-pc-linux-gnu-gcc: scipy/linsolve/_zsuperlumodule.c In file included from scipy/linsolve/_superluobject.h:9, from scipy/linsolve/_zsuperlumodule.c:33: scipy/linsolve/SuperLU/SRC/scomplex.h:60: error: conflicting types for ‘_Py_c_abs’ /usr/include/python2.6/complexobject.h:30: error: previous declaration of ‘_Py_c_abs’ was here In file included from scipy/linsolve/_superluobject.h:9, from scipy/linsolve/_zsuperlumodule.c:33: scipy/linsolve/SuperLU/SRC/scomplex.h:60: error: conflicting types for ‘_Py_c_abs’ /usr/include/python2.6/complexobject.h:30: error: previous declaration of ‘_Py_c_abs’ was here error: Command "x86_64-pc-linux-gnu-gcc -pthread -fno-strict-aliasing -march=nocona -O2 -pipe -fPIC -DATLAS_INFO="\"3.9.3\"" -DUSE_VENDOR_BLAS=1 -I/usr/lib64/python2.6/site-packages/numpy/core/include -I/usr/include/python2.6 -c scipy/linsolve/_zsuperlumodule.c -o build/temp.linux-x86_64-2.6/scipy/linsolve/_zsuperlumodule.o" failed with exit status 1 Reproducible: Always
emerge --info Portage 2.2_rc12 (default/linux/amd64/2008.0, gcc-4.3.2, glibc-2.8_p20080602-r0, 2.6.27-gentoo x86_64) ================================================================= System uname: Linux-2.6.27-gentoo-x86_64-Intel-R-_Core-TM-2_CPU_T5500_@_1.66GHz-with-gentoo-2.0.0 Timestamp of tree: Thu, 30 Oct 2008 18:37:02 +0000 ccache version 2.4 [enabled] app-shells/bash: 3.2_p39 dev-java/java-config: 1.3.7, 2.1.6-r1 dev-lang/python: 2.4.4-r15, 2.5.2-r8, 2.6-r4 dev-python/pycrypto: 2.0.1-r6 dev-util/ccache: 2.4-r7 dev-util/cmake: 2.6.2 sys-apps/baselayout: 2.0.0 sys-apps/openrc: 0.3.0-r1 sys-apps/sandbox: 1.2.18.1-r3 sys-devel/autoconf: 2.13, 2.63 sys-devel/automake: 1.5, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.1-r1 sys-devel/binutils: 2.18-r3 sys-devel/gcc-config: 1.4.0-r4 sys-devel/libtool: 2.2.6a virtual/os-headers: 2.6.27-r2 ACCEPT_KEYWORDS="amd64 ~amd64" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=nocona -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/config" 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/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/ext-active/ /etc/revdep-rebuild /etc/splash /etc/terminfo /etc/texmf/web2c /etc/udev/rules.d" CXXFLAGS="-march=nocona -O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="ccache collision-protect distlocks parallel-fetch preserve-libs protect-owned sandbox sfperms strict unmerge-orphans userfetch" GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo" LANG="en_US.utf8" LDFLAGS="-Wl,-O1" MAKEOPTS="-j3" PKGDIR="/usr/portage/packages" 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/kdesvn-portage /usr/portage/local" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="acl acpi alsa amd64 bash-completion berkdb bitmap-fonts bzip2 cli cracklib crypt cups dbus dri fortran gdbm gpm hal htmlhandbook iconv isdnlog midi mmx mudflap multilib ncurses nls nptl nptlonly opengl openmp pam pcre perl pppd python readline reflection session spl sse sse2 ssl sysfs tcpd truetype-fonts type1-fonts unicode vim-syntax xcomposite xorg zlib" ALSA_CARDS="hda-intel" 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 synaptics wacom" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" USERLAND="GNU" VIDEO_CARDS="nvidia" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Created attachment 170429 [details] complete build.log
If this bug report is correct, it should block bug #230205.
Created attachment 171446 [details, diff] rename c_abs* to slu_c_abs* From /usr/include/python2.6/complexobject.h (line 22): #define c_abs _Py_c_abs This conflicts with the c_abs function defined in scipy/linsolve/SuperLU/SRC/scomplex.{c,h} Upstream solved this by renaming c_abs* to slu_cabs*, see http://www.scipy.org/scipy/scipy/changeset/4767 http://www.scipy.org/scipy/scipy/changeset/4768 Attached patch fixes the build error for me, however running scipy.test() gives 2 failures and 92 errors, lots of deprecation warnings and a RuntimeError related to atexit.
fixed. thanks.
