* Package: sci-chemistry/openbabel-python-2.3.2 * Repository: gentoo * Maintainer: sci-chemistry@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux python_targets_python2_7 python_targets_python3_3 userland_GNU * FEATURES: preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking openbabel-2.3.2.tar.gz to /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work >>> Source unpacked in /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work >>> Preparing source in /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2 ... * Applying openbabel-python-2.3.2-testpybel.patch ... [ ok ] * Applying openbabel-python-2.3.2-bindings_only.patch ... [ ok ] scripts/openbabel-python.i:230: Error: Unknown SWIG preprocessor directive: CloneData scripts/openbabel-python.i:292: Error: Unknown SWIG preprocessor directive: Ignore scripts/openbabel-python.i:313: Error: Unknown SWIG preprocessor directive: Ignore scripts/openbabel-python.i:324: Error: Unknown SWIG preprocessor directive: The scripts/openbabel-python.i:325: Error: Unknown SWIG preprocessor directive: This scripts/openbabel-python.i:326: Error: Unknown SWIG preprocessor directive: the scripts/openbabel-python.i:327: Error: Unknown SWIG preprocessor directive: the scripts/openbabel-python.i:328: Error: Unknown SWIG preprocessor directive: This scripts/openbabel-python.i:329: Error: Unknown SWIG preprocessor directive: pointers scripts/openbabel-python.i:330: Error: Unknown SWIG preprocessor directive: OBAtomIter scripts/openbabel-python.i:349: Error: Unknown SWIG preprocessor directive: These scripts/openbabel-python.i:350: Error: Unknown SWIG preprocessor directive: classes scripts/openbabel-python.i:370: Error: Unknown SWIG preprocessor directive: The scripts/openbabel-python.i:371: Error: Unknown SWIG preprocessor directive: equivalent scripts/openbabel-python.i:462: Error: Unknown SWIG preprocessor directive: Copy scripts/openbabel-python.i:473: Error: Unknown SWIG preprocessor directive: Functions * ERROR: sci-chemistry/openbabel-python-2.3.2::gentoo failed (prepare phase): * Regeneration of openbabel-python.cpp failed * * Call stack: * ebuild.sh, line 93: Called src_prepare * environment, line 3909: Called die * The specific snippet of code: * swig -python -c++ -small -O -templatereduce -naturalvar -I"${EPREFIX}/usr/include/openbabel-2.0" -o scripts/python/openbabel-python.cpp -DHAVE_EIGEN -outdir scripts/python scripts/openbabel-python.i || die "Regeneration of openbabel-python.cpp failed" * * If you need support, post the output of `emerge --info '=sci-chemistry/openbabel-python-2.3.2::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-chemistry/openbabel-python-2.3.2::gentoo'`. * The complete build log is located at '/var/log/portage/sci-chemistry:openbabel-python-2.3.2:20150110-094654.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/temp/environment'. * Working directory: '/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2' * S: '/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2' * GNU info directory index is up-to-date. * IMPORTANT: 2 config files in '/etc' need updating. * See the CONFIGURATION FILES section of the emerge * man page to learn how to update config files. This chroot image is located at a hardened amd64 host. Portage 2.2.15 (python 2.7.9-final-0, default/linux/amd64/13.0, gcc-4.8.4, glibc-2.20-r1, 3.17.7-hardened-r1 x86_64) ================================================================= System uname: Linux-3.17.7-hardened-r1-x86_64-Intel-R-_Core-TM-_i7-3770_CPU_@_3.40GHz-with-gentoo-2.2 KiB Mem: 16166924 total, 1676528 free KiB Swap: 16777212 total, 16762980 free Timestamp of tree: Sat, 10 Jan 2015 08:45:01 +0000 sh bash 4.3_p33 ld GNU ld (Gentoo 2.24 p1.4) 2.24 app-shells/bash: 4.3_p33 dev-java/java-config: 2.2.0 dev-lang/perl: 5.20.1-r4 dev-lang/python: 2.7.9-r1, 3.3.5-r1 dev-util/cmake: 3.0.2 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.13.6 sys-apps/sandbox: 2.6-r1 sys-devel/autoconf: 2.69 sys-devel/automake: 1.11.6-r1, 1.15 sys-devel/binutils: 2.24-r3 sys-devel/gcc: 4.8.4 sys-devel/gcc-config: 1.8 sys-devel/libtool: 2.4.4 sys-devel/make: 4.1-r1 sys-kernel/linux-headers: 3.18 (virtual/os-headers) sys-libs/glibc: 2.20-r1 Repositories: gentoo ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt /var/spool/torque" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /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="-O2 -pipe" DISTDIR="/usr/portage/distfiles" EMERGE_DEFAULT_OPTS="--nospinner --tree --quiet-build --deep --jobs 1" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://mirror.leaseweb.com/gentoo/ http://ftp.uni-erlangen.de/pub/mirrors/gentoo http://ftp-stud.hs-esslingen.de/pub/Mirrors/gentoo/ http://gd.tuwien.ac.at/opsys/linux/gentoo/" LANG="en_US.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j1" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-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="" SYNC="rsync://rsync.de.gentoo.org/gentoo-portage" USE="acl amd64 berkdb bindist bzip2 cli cracklib crypt cxx dri fortran gdbm iconv ipv6 mbox mmx modules multilib ncurses nls nptl openmp pam pax_kernel pcre readline session sse sse2 ssl tcpd unicode 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" 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 ublox ubx" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" RUBY_TARGETS="ruby19 ruby20" USERLAND="GNU" VIDEO_CARDS="fbdev glint intel mach64 mga nouveau nv r128 radeon savage sis tdfx trident vesa via vmware dummy 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, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
which swig version are you using?
Created attachment 393690 [details] emerge log (In reply to Justin Lecher from comment #1) > which swig version are you using? it is a QA chroot system - so what I do have, is the current emerge log (attached), but probably this might help: /var/log/portage/dev-lang:swig-3.0.3:20150110-080817.log
(In reply to Toralf Förster from comment #2) > Created attachment 393690 [details] > emerge log > > (In reply to Justin Lecher from comment #1) > > which swig version are you using? > > it is a QA chroot system - so what I do have, is the current emerge log > (attached), but probably this might help: Still it works for me, so there is something at your side. Which swig version is this?
+ 11 Jan 2015; Justin Lecher <jlec@gentoo.org> openbabel-python-2.3.2.ebuild, + +files/openbabel-python-2.3.2-swig-3.0.3.patch: + Fix for swig-3.0.3, #536180 +
