'emerge pygsl' fails with: ... x86_64-pc-linux-gnu-gcc -pthread -shared -Wl,-O1 -march=nocona -O3 -pipe -fomit-frame-pointer build/temp.linux-x86_64-2.6/src/simanmodule.o -L/usr/lib -L/usr/lib64 -lgsl -lgslcblas -lm -lpython2.6 -o build/lib.linux-x86_64-2.6/pygsl/_siman.so building 'const' extension C compiler: x86_64-pc-linux-gnu-gcc -pthread -DNDEBUG -march=nocona -O3 -pipe -fomit-frame-pointer -fPIC compile options: '-DSWIG_COBJECT_TYPES=1 -DDEBUG=1 -DNUMERIC=1 -DPYGSL_GSL_MAJOR_VERSION=1 -DPYGSL_GSL_MINOR_VERSION=13 -UNDEBUG -I/usr/include -IInclude -I. -I/usr/lib64/python2.6/site-packages/numpy/core/include -I/usr/include/python2.6 -c' x86_64-pc-linux-gnu-gcc: src/constmodule.c In file included from src/constmodule.c:58: src/const_cgs_array.c:17: error: 'GSL_CONST_CGS_BOHR_MAGNETON' undeclared here (not in a function) src/const_cgs_array.c:18: error: 'GSL_CONST_CGS_NUCLEAR_MAGNETON' undeclared here (not in a function) src/const_cgs_array.c:19: error: 'GSL_CONST_CGS_ELECTRON_MAGNETIC_MOMENT' undeclared here (not in a function) src/const_cgs_array.c:20: error: 'GSL_CONST_CGS_PROTON_MAGNETIC_MOMENT' undeclared here (not in a function) src/const_cgs_array.c:79: error: 'GSL_CONST_CGS_FARADAY' undeclared here (not in a function) src/const_cgs_array.c:80: error: 'GSL_CONST_CGS_ELECTRON_CHARGE' undeclared here (not in a function) src/const_cgs_array.c:81: error: 'GSL_CONST_CGS_GAUSS' undeclared here (not in a function) In file included from src/constmodule.c:72: src/const_cgsm_array.c:80: error: 'GSL_CONST_CGSM_GAUSS' undeclared here (not in a function) src/const_cgsm_array.c:80: error: initializer element is not constant src/const_cgsm_array.c:80: error: (near initialization for 'cgsm_array[79].value') In file included from src/constmodule.c:58: src/const_cgs_array.c:17: error: 'GSL_CONST_CGS_BOHR_MAGNETON' undeclared here (not in a function) src/const_cgs_array.c:18: error: 'GSL_CONST_CGS_NUCLEAR_MAGNETON' undeclared here (not in a function) src/const_cgs_array.c:19: error: 'GSL_CONST_CGS_ELECTRON_MAGNETIC_MOMENT' undeclared here (not in a function) src/const_cgs_array.c:20: error: 'GSL_CONST_CGS_PROTON_MAGNETIC_MOMENT' undeclared here (not in a function) src/const_cgs_array.c:79: error: 'GSL_CONST_CGS_FARADAY' undeclared here (not in a function) src/const_cgs_array.c:80: error: 'GSL_CONST_CGS_ELECTRON_CHARGE' undeclared here (not in a function) src/const_cgs_array.c:81: error: 'GSL_CONST_CGS_GAUSS' undeclared here (not in a function) In file included from src/constmodule.c:72: src/const_cgsm_array.c:80: error: 'GSL_CONST_CGSM_GAUSS' undeclared here (not in a function) src/const_cgsm_array.c:80: error: initializer element is not constant src/const_cgsm_array.c:80: error: (near initialization for 'cgsm_array[79].value') error: Command "x86_64-pc-linux-gnu-gcc -pthread -DNDEBUG -march=nocona -O3 -pipe -fomit-frame-pointer -fPIC -DSWIG_COBJECT_TYPES=1 -DDEBUG=1 -DNUMERIC=1 -DPYGSL_GSL_MAJOR_VERSION=1 -DPYGSL_GSL_MINOR_VERSION=13 -UNDEBUG -I/usr/include -IInclude -I. -I/usr/lib64/python2.6/site-packages/numpy/core/include -I/usr/include/python2.6 -c src/constmodule.c -o build/temp.linux-x86_64-2.6/src/constmodule.o" failed with exit status 1 * * ERROR: dev-python/pygsl-0.9.4 failed. Reproducible: Always root@lynx:/usr/local/portage/dev-python(45)# emerge --info Portage 2.1.6.13 (default/linux/amd64/2008.0/desktop, gcc-4.4.1, glibc-2.10.1-r0, 2.6.31-gentoo x86_64) ================================================================= System uname: Linux-2.6.31-gentoo-x86_64-Intel-R-_Core-TM-2_Duo_CPU_T8300_@_2.40GHz-with-gentoo-2.0.1 Timestamp of tree: Fri, 25 Sep 2009 08:00:01 +0000 app-shells/bash: 4.0_p33 dev-java/java-config: 2.1.9-r1 dev-lang/python: 2.6.2-r2, 3.1.1-r1 dev-python/pycrypto: 2.0.1-r8 dev-util/cmake: 2.6.4-r2 sys-apps/baselayout: 2.0.1 sys-apps/openrc: 0.4.3-r3 sys-apps/sandbox: 2.1 sys-devel/autoconf: 2.13, 2.63-r1 sys-devel/automake: 1.4_p6, 1.5, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.2, 1.11 sys-devel/binutils: 2.19.1-r1 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.6a virtual/os-headers: 2.6.30-r1 ACCEPT_KEYWORDS="amd64 ~amd64" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=nocona -O3 -pipe -fomit-frame-pointer" 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 /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/eselect/postgresql /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/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c /etc/udev/rules.d" CXXFLAGS="-march=nocona -O3 -pipe -fomit-frame-pointer" DISTDIR="/usr/portage/distfiles" FEATURES="distlocks fixpackages parallel-fetch protect-owned sandbox sfperms strict unmerge-orphans userfetch" FFLAGS="-march=nocona -O3 -pipe -fomit-frame-pointer" GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo" LDFLAGS="-Wl,-O1" LINGUAS="de fr" MAKEOPTS="-j1" 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/local/portage/layman/n4g /usr/local/portage/layman/dotnet /usr/local/portage/layman/science /usr/local/portage/layman/java-overlay /usr/local/portage/layman/suka /usr/local/portage/layman/zugaina /usr/local/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X Xaw3d a52 aac acl acpi administrator afs aiglx alsa amd64 amrr ao aotuv apache2 asf aspell atlas auctex audacious audiofile automount bash-completion beagle berkdb bjam blas bluetooth bonobo boo boost branding bzip2 c++ cairo cardbus cdda cddb cdf cdio cdparanoia cdr cgi chm cli consolekit corba cracklib cran crypt cups curl cxx daap dbus device-mapper dga dia divx djvu dlloader dmi doc dri ds3490 dts dv dvb dvd dvdr dvi dxr3 dynagraph eds effects elf emacs emboss encode epiphany esd evo examples exif expat extra extras fam fame ffmpeg fftw firefox fits flac fltk foomaticdb fortran fpx fuse galago garmin gd gdal gdbm geos gif gimp gimpprint ginac glade glib glitz gml gmp gnokii gnome gnome-keyring gnuplot gnutls gphoto2 gpm graphics graphviz gs gsl gsm gstreamer gtk guile hal hardened harness hddtemp hdf hdf5 hlapi http httpd hvm iconv icq icu id3 ide imagemagick imap innodb ipod ipv6 irda irmc isdnlog ithreads jabber java java5 java6 jbig john jpeg jpeg2k kde kde4 kerberos kexi keyring kvm ladspa lame lapack laptop latex lcms ldap libffi libgda libnotify libsamplerate lirc lua lzo lzw mad maildir mailwrapper math matroska mikmod mmx mmxext mng mod modules mono motif mozdevelop mozilla mozsvg mozxmlterm mp3 mp4 mp4live mpeg mpeg2 mplayer mtp mudflap multilib musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networkmanager nfs nls nntp nptl nptlonly nsplugin ntfs ntp numarray numeric obex objc ocaml octave odbc ogdi ogg ole openexr opengl openmp pae pam pcre pda pdf perl pipechan plotutils plugins png podcast policykit posix postgres postscript ppds pppd preview-latex proj projectx pstricks pulseaudio python qhull qt3 qt3support qt4 quicktime readline reflection reiserfs rhythmbox rle rpc rrdcgi rrdtool samba sasl science sdl server session slang slp smp sndfile snmp soup sox speex spell spl sql sqlite sse sse2 ssl startup-notification stlport subtitles subversion suexec svg sysfs szip t1lib tcl tcpd tex theora threads thunar thunderbird tidy tiff tk tntc truetype unicode usb userlocales utempter v4l2 vorbis wav webdav webdav-serf webkit wifi wmf wxwidgets x264 xattr xcb xemacs xext xine xml xmlreader xmlrpc xorg xpm xulrunner xv xvid xvmc zlib zvbi" ALSA_CARDS="intel8x0" 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 auth_digest authn_anon authn_dbd 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 dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif so speling status unique_id userdir usertrack vhost_alias" DVB_CARDS="usb-wt220u" ELIBC="glibc" INPUT_DEVICES="keyboard mouse synaptics " KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="de fr" NETBEANS_MODULES="ide websvccommon nb harness apisupport groovy gsf j2ee java xml" USERLAND="GNU" VIDEO_CARDS="nv vesa" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Your version of sci-libs/gsl? I guess it needs a newer version.
root@lynx:/usr/src(58)# qlist -Iv gsl dev-python/pygsl-0.9.4 sci-libs/gsl-1.13-r1 sci-mathematics/octave-forge-gsl-1.0.7
Also reemerging of sci-libs/gsl does not help: root@lynx:/usr/src(60)# genlop -t sci-libs/gsl | tail Mon Sep 21 10:47:54 2009 >>> sci-libs/gsl-1.13-r1 merge time: 4 minutes and 39 seconds. Sun Sep 27 04:45:24 2009 >>> sci-libs/gsl-1.13-r1 merge time: 3 minutes and 53 seconds. Sun Sep 27 13:43:48 2009 >>> sci-libs/gsl-1.13-r1 merge time: 5 minutes and 15 seconds.
Created attachment 205459 [details, diff] adding patch for newer version of gsl
Created attachment 205461 [details, diff] removing obsolete units
(In reply to comment #1) > Your version of sci-libs/gsl? I guess it needs a newer version. Quite the opposite. Those units were removed in 1.13. See http://www.gnu.org/software/gsl/NEWS Guess GSL maintainers don't like astrophysicists, we still use 'gausses' ;(
Hallo Kasper, after using your patch 'emerge pygsl' fails with: ... * checking miscfile checksums ;-) ... [ ok ] >>> Unpacking source... >>> Unpacking pygsl-0.9.4.tar.gz to /var/tmp/portage/dev-python/pygsl-0.9.4/work ERROR: Invalid atom: '>=sci-libs/gsl-1.13*'
If I change pygsl-0.9.4.diff a little bit to pygsl-0.9.4_new.diff, 'emerge -v1 pygsl' does a step more, and then fails with: ... >>> Unpacking pygsl-0.9.4.tar.gz to /var/tmp/portage/dev-python/pygsl-0.9.4/work * Applying pygsl-0.9.4-obsolete-units.patch ... * Failed Patch: pygsl-0.9.4-obsolete-units.patch ! * ( /usr/local/portage/dev-python/pygsl/files/pygsl-0.9.4-obsolete-units.patch ) * * Include in your bugreport the contents of: * * /var/tmp/portage/dev-python/pygsl-0.9.4/temp/pygsl-0.9.4-obsolete-units.patch-18997.out
Created attachment 205478 [details, diff] adding patch for newer version of gsl Sorry my bad. Now should be fine, please try again.
Created attachment 205480 [details] pygsl-0.9.4_new.diff
Created attachment 205481 [details] pygsl-0.9.4-obsolete-units.patch-18997.out
Hallo Kasper, pygsl-0.9.4_new.diff and your new version of pygsl-0.9.4.diff is almost identical, so I suppose I get the same error with your diff file. Do you still have an idea? Regards Juergen
Created attachment 205482 [details, diff] removing obsolete units
Diff shows that the new patch of Comment #13 and the old patch of Comment #5 are identical. root@lynx:/usr/local/portage/dev-python/pygsl(110)# diff /home_grizzly/rose/Txt/Patches/pygsl-0.9.4-obsolete-units.patch files/pygsl-0.9.4-obsolete-units.patch root@lynx:/usr/local/portage/dev-python/pygsl(111)#
Created attachment 205483 [details, diff] removing obsolete units
(In reply to comment #14) > Diff shows that the new patch of Comment #13 and the old patch of Comment #5 > are identical. Sorry for the mess. It should be working now
Thanks Kaspar, now it works.
fixed. Thanks!
