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Bug 472900 - [science overlay] sci-chemistry/nwchem-6.3[python] - Failed Patch: nwchem-6.1.1-python_makefile.patch
Summary: [science overlay] sci-chemistry/nwchem-6.3[python] - Failed Patch: nwchem-6.1...
Status: RESOLVED OBSOLETE
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Related Packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2013-06-10 18:04 UTC by Michelangelo Scopelliti
Modified: 2015-08-04 20:17 UTC (History)
0 users

See Also:
Package list:
Runtime testing required: ---


Attachments
patch output (nwchem-6.1.1-python_makefile.patch.out,2.99 KB, text/plain)
2013-06-10 18:06 UTC, Michelangelo Scopelliti
Details
build log (build.log.gz,1.51 KB, application/gzip)
2013-06-10 18:06 UTC, Michelangelo Scopelliti
Details

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Description Michelangelo Scopelliti 2013-06-10 18:04:50 UTC
USE=python causes nwchem build to fail.
The ebuild is unable to apply nwchem-6.1.1-python_makefile.patch


Reproducible: Always




emerge -pqv '=sci-chemistry/nwchem-6.3'

[ebuild   R   ] sci-chemistry/nwchem-6.3  USE="mpi python* -doc -examples -nwchem-tests" PYTHON_SINGLE_TARGET="python2_7 -python2_6" PYTHON_TARGETS="python2_7 -python2_6" 



emerge --info '=sci-chemistry/nwchem-6.3'

Portage 2.2.0_alpha179 (default/linux/amd64/13.0, gcc-4.7.3, glibc-2.17, 3.9.5 x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-3.9.5-x86_64-AMD_Phenom-tm-_II_X6_1055T_Processor-with-gentoo-2.2
KiB Mem:     7654320 total,   5794592 free
KiB Swap:     524284 total,    524284 free
Timestamp of tree: Mon, 10 Jun 2013 15:45:01 +0000
ld ld di GNU (GNU Binutils) 2.23.1
app-shells/bash:          4.2_p45
dev-java/java-config:     2.2.0
dev-lang/python:          2.7.5, 3.3.2
dev-util/cmake:           2.8.11.1
dev-util/pkgconfig:       0.28
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.11.8
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.11.6, 1.13.2
sys-devel/binutils:       2.23.1
sys-devel/gcc:            4.7.3
sys-devel/gcc-config:     1.8
sys-devel/libtool:        2.4.2
sys-devel/make:           3.82-r4
sys-kernel/linux-headers: 3.9 (virtual/os-headers)
sys-libs/glibc:           2.17
Repositories: gentoo science kernelpanic
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA @EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
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/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.5/ext-active/ /etc/php/cgi-php5.5/ext-active/ /etc/php/cli-php5.5/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"
CXXFLAGS="-march=native -O2 -pipe"
DISTDIR="/var/portage/distfiles"
FCFLAGS="-march=native -O2 -pipe"
FEATURES="assume-digests binpkg-logs candy clean-logs compress-build-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch parallel-install preserve-libs protect-owned sandbox sfperms split-elog split-log strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-march=native -O2 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="it_IT.UTF-8"
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 --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/var/lib/layman/science /usr/local/portage"
SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage"
USE="3dnow 3dnowext SECURITY_HAZARD X a52 aac aalib acl adolc aio alisp alsa amd64 amr anacron ao apng audiofile bazaar berkdb bidi bitmap bittorrent blas branding bs2b bufferevents bzip2 cairo caps cblas-external cdda cdio chm cjk cli clucene compact conntrack consolekit context contrast contrib corefonts cracklib crypt cups curl cvs cxx dbus demosaic detex device-mapper devil dga dhcp dhcp-tools dia djbfft djvu dri dts dv dvb dvd dvi2tty dvipdfm ebook ecdsa eigen emf encode epspdf excel exif extensions extra extra-tools extras faac facedetect fdformat ffmpeg fftw firmware fits flac fluidsynth fontconfig fontforge fortran fpx frei0r ftp gbm gcj gd gdbm geoip gif gimp git glamor glut gmp gold gost gpg gphoto2 gpm graphics graphicsmagick graphite graphviz gsl gsm gstreamer gtk gtk2 gtkstyle gts gudev hdri highlight hpn humanities hwdb iconv icu id3tag idn imagemagick imaging inkjar inotify ios ipv6 ipython ithreads jadetex jbig jemalloc jpeg jpeg2k kdrive keymap kmod kpathsea ladspa lame lapack lasi latex lcms ldns lensfun libass libcaca libkms libnl libnotify libproxy libsamplerate libv4l llvm lpsol lqr lto lua luatex lynxkeymap lzma lzo mad math mathml matplotlib matroska mdev mem-scramble mercurial metalink metapost metis metric midi minizip mjpeg mmap mms mmx mmxext mng mod modplug modules mount mp3 mp3rtp mpeg mpi mpi-threads mudflap multicall multilib multitarget musepack music musicbrainz mysql mysqli nat-pmp natspec ncat ncurses ndiff netlink nettle network network-cron networking newnet nls normalize nping nptl nsplugin ntfs numpy nut nuv ocr odk offensive offlinehelp ofx ogg openal openexr opengl openmp openvg opus osmesa pam pango passwdqc pch pcre pdf pdo pgf pkcs11 plotutils plugins png pnm policykit postgres postproc postscript pstricks publishers pvr pyglet python python3 q16 q32 q64 q8 qt3support quicktime quvi rar raw readline reencrypt reiserfs replaygain rle rpc rtmp scale0tilt scanner schroedinger science script sdl secure-delete secure-messaging session smartcard smi smp sndfile sox sparse speex spell spoof-source sql sqlite sse sse2 sse3 ssl startup-notification subversion suid svg syslog system-cairo system-jpeg system-sqlite t1lib taglib tcl telepathy tftp tga theora thin-splines threads tiff timezone tk tls tools transparent-proxy truetype tty-helpers twolame type3 udev udis86 udisks umfpack unicode urandom usb utils v4l vaapi vcd vdpau video vim vim-syntax vorbis vpx wavpack wayland web webdav webgl webp wmf wxwidgets x264 xa xanim xattr xcb xcomposite xdg xetex xft xkb xml xmlrpc xmp xorg xpm xscreensaver xv xvid xvmc yuv4mpeg zlib" ABI_X86="64" 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" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd 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 sheets stage tables krita karbon braindump author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CURL_SSL="gnutls" ELIBC="glibc" FOO2ZJS_DEVICES="sa300" 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" LIBREOFFICE_EXTENSIONS="nlpsolver presenter-minimizer scripting-beanshell wiki-publisher" LINGUAS="it en fr" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" QEMU_SOFTMMU_TARGETS="arm i386 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby19" SANE_BACKENDS="xerox_mfp" USERLAND="GNU" VIDEO_CARDS="r600 radeon 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, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON

=================================================================
                        Package Settings
=================================================================
USE="mpi -doc -examples -nwchem-tests -python" PYTHON_SINGLE_TARGET="python2_7 -python2_6" PYTHON_TARGETS="python2_7 -python2_6"

sci-chemistry/nwchem-6.3 was built with the following:
Comment 1 Michelangelo Scopelliti 2013-06-10 18:06:13 UTC
Created attachment 350702 [details]
patch output
Comment 2 Michelangelo Scopelliti 2013-06-10 18:06:47 UTC
Created attachment 350704 [details]
build log
Comment 3 Marius Brehler 2015-08-04 20:17:07 UTC
Not an issue for nwchem-6.3_p2-r1 anymore.


marbre ~/sci/sci-chemistry/nwchem $ USE="python" ebuild nwchem-6.3_p2-r1.ebuild prepare
Appending /home/marbre/sci to PORTDIR_OVERLAY...
 * Nwchem-6.3.revision2-src.2013-10-17.tar.gz SHA256 SHA512 WHIRLPOOL size ;-) ...                       [ ok ]
 * Using following Fortran compiler:
 *   F77: mpif77
 *   FC:  mpif90
 * mpif90 has OPENMP support
/var/tmp/portage/sci-chemistry/nwchem-6.3_p2-r1/temp /usr/lib64/python3.3/site-packages
/usr/lib64/python3.3/site-packages
>>> Unpacking source...
>>> Unpacking Nwchem-6.3.revision2-src.2013-10-17.tar.gz to /var/tmp/portage/sci-chemistry/nwchem-6.3_p2-r1/work
>>> Source unpacked in /var/tmp/portage/sci-chemistry/nwchem-6.3_p2-r1/work
>>> Preparing source in /var/tmp/portage/sci-chemistry/nwchem-6.3_p2-r1/work/nwchem ...
 * Applying nwchem-6.1.1-makefile.patch ...                                                              [ ok ]
 * Applying nwchem-6.1.1-nwchemrc.patch ...                                                              [ ok ]
 * Applying nwchem-6.1.1-adjust-dir-length.patch ...                                                     [ ok ]
 * Applying nwchem-6.1.1-python_makefile.patch ...                                                       [ ok ]
>>> Source prepared.