'emerge openbabel' fails with: ... make: Nothing to be done for `scripts/python/openbabel_python.cpp'. * Building of sci-chemistry/openbabel-2.2.3 with CPython 2.6... python2.6 setup.py build -b build-2.6 WARNING: Environment variable OPENBABEL_INSTALL is not set INFO: Looking for library and include files in ../../src and ../../include running build running build_py creating build-2.6 creating build-2.6/lib.linux-i686-2.6 copying openbabel.py -> build-2.6/lib.linux-i686-2.6 copying pybel.py -> build-2.6/lib.linux-i686-2.6 warning: build_py: byte-compiling is disabled, skipping. running build_ext building '_openbabel' extension creating build-2.6/temp.linux-i686-2.6 i686-pc-linux-gnu-g++ -pthread -O2 -march=pentium4 -fomit-frame-pointer -fPIC -I../../include -I/usr/include/python2.6 -c openbabel_python.cpp -o build-2.6/temp.linux-i686-2.6/openbabel_python.o i686-pc-linux-gnu-g++ -pthread -shared -Wl,-O1 -O2 -march=pentium4 -fomit-frame-pointer build-2.6/temp.linux-i686-2.6/openbabel_python.o -L../../src/.libs -L/usr/lib -lopenbabel -lpython2.6 -o build-2.6/lib.linux-i686-2.6/_openbabel.so >>> Source compiled. >>> Test phase [not enabled]: sci-chemistry/openbabel-2.2.3 >>> Install openbabel-2.2.3 into /var/tmp/portage/sci-chemistry/openbabel-2.2.3/image/ category sci-chemistry install: cannot stat `API/html/*': No such file or directory !!! doins: API/html/* does not exist * ERROR: sci-chemistry/openbabel-2.2.3 failed: Reproducible: Always root@tiger:/usr/local/portage/app-admin/conky(31)# emerge --info =sci-chemistry/openbabel-2.2.3 Portage 2.1.8.3 (default/linux/x86/10.0/desktop, gcc-4.4.3, glibc-2.11.1-r0, 2.6.34 i686) ================================================================= System Settings ================================================================= System uname: Linux-2.6.34-i686-Intel-R-_Pentium-R-_4_CPU_1.60GHz-with-gentoo-2.0.1 Timestamp of tree: Thu, 03 Jun 2010 05:05:01 +0000 distcc 3.1 i686-pc-linux-gnu [disabled] app-shells/bash: 4.1_p7 dev-java/java-config: 2.1.11 dev-lang/python: 2.6.5-r2, 3.1.2-r3 dev-python/pycrypto: 2.1.0 dev-util/cmake: 2.8.1-r2 sys-apps/baselayout: 2.0.1 sys-apps/openrc: 0.6.1-r1 sys-apps/sandbox: 2.2 sys-devel/autoconf: 2.13, 2.65 sys-devel/automake: 1.4_p6, 1.7.9-r2, 1.8.5-r3, 1.9.6-r3, 1.10.3, 1.11.1 sys-devel/binutils: 2.20.1-r1 sys-devel/gcc: 4.4.3-r2 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.7b virtual/os-headers: 2.6.33 ACCEPT_KEYWORDS="x86 ~x86" ACCEPT_LICENSE="* -@EULA PUEL dlj-1.1 skype-eula" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -march=pentium4 -fomit-frame-pointer" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/X11/xkb /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" CXXFLAGS="-O2 -march=pentium4 -fomit-frame-pointer" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests distlocks fixpackages news parallel-fetch protect-owned sandbox sfperms strict unmerge-logs unmerge-orphans userfetch" FFLAGS="-O2 -march=pentium4 -fomit-frame-pointer" GENTOO_MIRRORS="ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror/ http://ftp.uni-erlangen.de/pub/mirrors/gentoo ftp://ftp.uni-erlangen.de/pub/mirrors/gentoo ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo ftp://ftp.join.uni-muenster.de/pub/linux/distributions/gentoo http://mirrors.sec.informatik.tu-darmstadt.de/gentoo/ http://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/ " LDFLAGS="-Wl,-O1" LINGUAS="de fr" 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="/var/lib/layman/science /var/lib/layman/java-overlay /var/lib/layman/zugaina /var/lib/layman/x11 /var/lib/layman/sunrise /usr/local/portage /var/lib/cpan" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X Xaw3d a52 aac abiword acl acpi afs alsa ao apache2 applet archive arpack asf aspell assistant audacious audiofile automap automount bash-completion beagle berkdb blas blast bluetooth boo boost branding bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cgi chm cli consolekit corba cracklib crypt css cups curl cxx daap db dbase dbi dbm dbus designer devhelp device-mapper dga dia djvu doc dri ds2490 dts dv dvb dvd dvdr dvi eds elf emacs emboss empathy encode epiphany evo examples exif expat extensions extra extras fam fame ffmpeg fftw firefox fits flac fltk foomaticdb fortran fpx fts3 fuse galago gcj gd gdal gdbm gedit geoip geolocation geos gif gimp ginac git glade glib glitz gml gmp gmtsuppl gnokii gnome gnome-keyring gnome-print gnuplot gnutls gphoto2 gpm grammar graphics graphtft graphviz grass gs gsl gsm gstreamer gtk guile hal harness hddtemp hdf hdf5 hdri hlapi http httpd iconv icq icu id3 ide imagemagick imap innodb inotify ipod ipv6 irda ithreads jabber jadetex java java5 java6 jbig john jpeg jpeg2k kdrive kerberos kpathsea kqemu ladspa lame lapack latex latex3 lcms ldap lensfun libffi libgda libnotify libsamplerate lirc lm_sensors lua lzo mad mail maildir mailwrapper mapnik math matroska mikmod mkl mmx mmxext mng modules mono moonlight motif mozdevelop mozilla mp3 mp4 mpeg mplayer mtp mudflap musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking networkmanager nfs nls nntp nptl nptlonly nsplugin ntfs ntp numarray numeric obex objc ocaml octave odbc ogdi ogg ole openexr opengl openmp overview pae pam pango pcre pda pdf perl plotutils plugins png podcast policykit posix postgres postscript ppds pppd preview-latex proj projectx pstricks pulseaudio pymol python python-bindings qemu qhull qt3support qt4 quicktime readline reflection reiserfs rle rpc rrdcgi rrdtool samba sasl science sdl secure-delete semantic-desktop server session sip slang slp smbclient smp sms sndfile snmp soup sox speex spell spl sql sqlite sse sse2 ssl startup-notification stlport subtitles subversion suexec svg swig sysfs szip t1lib tcl tcpd tex tex4ht texmacs theora threads thunderbird tidy tiff tk tntc tools truetype udev unicode usb userlocales utempter v4l2 virtualbox vorbis wav webdav webdav-serf webkit win32codecs wmf wxwidgets x264 x86 xattr xcb xemacs xext xine xml xmlreader xmlrpc xorg xpm xulrunner xv xvid xvmc zlib zvbi" ALSA_CARDS="via82xx" 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" CAMERAS="canon" DVB_CARDS="tda10045 tda10046lifeview" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev " KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="de fr" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler ruby websvccommon xml" QEMU_SOFTMMU_TARGETS="i386 ppc ppc64 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby18 jruby" USERLAND="GNU" VIDEO_CARDS="mga matrox vesa via openchrome" 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, LANG, LC_ALL, MAKEOPTS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS root@tiger:/usr/local/portage/app-admin/conky(32)# emerge -pqv =sci-chemistry/openbabel-2.2.3 [ebuild N ] sci-chemistry/openbabel-2.2.3 USE="doc python swig"
If fails on x86_64 systems, too.
On one x86_64 system I have for example: root@moose:/root(7)# emerge -v1 sci-chemistry/openbabel ... make -j3 docs (cd .; /usr/bin/doxygen) Warning: Tag `DETAILS_AT_TOP' at line 163 of file Doxyfile has become obsolete. To avoid this warning please update your configuration file using "doxygen -u" /var/tmp/portage/sci-chemistry/openbabel-2.2.3/work/openbabel-2.2.3/include/openbabel/math/spacegroup.h:91: Warning: included file I is not found. Check your EXAMPLE_PATH QGDict::hashAsciiKey: Invalid null key /var/tmp/portage/sci-chemistry/openbabel-2.2.3/work/openbabel-2.2.3/include/openbabel/dlhandler.h:59: Warning: Found unknown command `\lib' /var/tmp/portage/sci-chemistry/openbabel-2.2.3/work/openbabel-2.2.3/include/openbabel/dlhandler.h:59: Warning: Found unknown command `\openbabel' /var/tmp/portage/sci-chemistry/openbabel-2.2.3/work/openbabel-2.2.3/include/openbabel/dlhandler.h:59: Warning: Found unknown command `\BABEL_VERSION' /var/tmp/portage/sci-chemistry/openbabel-2.2.3/work/openbabel-2.2.3/include/openbabel/forcefield.h:875: Warning: argument 'gradients' of command @param is not found in the argument list of OBForceField::Energy(bool=true) /var/tmp/portage/sci-chemistry/openbabel-2.2.3/work/openbabel-2.2.3/include/openbabel/forcefield.h:885: Warning: argument 'gradients' of command @param is not found in the argument list of OBForceField::E_Bond(bool=true) /var/tmp/portage/sci-chemistry/openbabel-2.2.3/work/openbabel-2.2.3/include/openbabel/forcefield.h:892: Warning: argument 'gradients' of command @param is not found in the argument list of OBForceField::E_Angle(bool=true) /var/tmp/portage/sci-chemistry/openbabel-2.2.3/work/openbabel-2.2.3/include/openbabel/forcefield.h:899: Warning: argument 'gradients' of command @param is not found in the argument list of OBForceField::E_StrBnd(bool=true) /var/tmp/portage/sci-chemistry/openbabel-2.2.3/work/openbabel-2.2.3/include/openbabel/forcefield.h:906: Warning: argument 'gradients' of command @param is not found in the argument list of OBForceField::E_Torsion(bool=true) /var/tmp/portage/sci-chemistry/openbabel-2.2.3/work/openbabel-2.2.3/include/openbabel/forcefield.h:913: Warning: argument 'gradients' of command @param is not found in the argument list of OBForceField::E_OOP(bool=true) /var/tmp/portage/sci-chemistry/openbabel-2.2.3/work/openbabel-2.2.3/include/openbabel/forcefield.h:920: Warning: argument 'gradients' of command @param is not found in the argument list of OBForceField::E_VDW(bool=true) /var/tmp/portage/sci-chemistry/openbabel-2.2.3/work/openbabel-2.2.3/include/openbabel/forcefield.h:927: Warning: argument 'gradients' of command @param is not found in the argument list of OBForceField::E_Electrostatic(bool=true) make -j3 scripts/python/openbabel_python.cpp make: Nothing to be done for `scripts/python/openbabel_python.cpp'. * Building of sci-chemistry/openbabel-2.2.3 with CPython 2.6... python2.6 setup.py build -b build-2.6 WARNING: Environment variable OPENBABEL_INSTALL is not set INFO: Looking for library and include files in ../../src and ../../include running build running build_py creating build-2.6 creating build-2.6/lib.linux-x86_64-2.6 copying openbabel.py -> build-2.6/lib.linux-x86_64-2.6 copying pybel.py -> build-2.6/lib.linux-x86_64-2.6 warning: build_py: byte-compiling is disabled, skipping. running build_ext building '_openbabel' extension creating build-2.6/temp.linux-x86_64-2.6 x86_64-pc-linux-gnu-g++ -pthread -O2 -pipe -fPIC -I../../include -I/usr/include/python2.6 -c openbabel_python.cpp -o build-2.6/temp.linux-x86_64-2.6/openbabel_python.o x86_64-pc-linux-gnu-g++ -pthread -shared -Wl,-O1 -O2 -pipe build-2.6/temp.linux-x86_64-2.6/openbabel_python.o -L../../src/.libs -L/usr/lib64 -lopenbabel -lpython2.6 -o build-2.6/lib.linux-x86_64-2.6/_openbabel.so >>> Source compiled. >>> Test phase [not enabled]: sci-chemistry/openbabel-2.2.3 >>> Install openbabel-2.2.3 into /var/tmp/portage/sci-chemistry/openbabel-2.2.3/image/ category sci-chemistry install: cannot stat `API/html/*': No such file or directory !!! doins: API/html/* does not exist * ERROR: sci-chemistry/openbabel-2.2.3 failed: * (no error message) * * Call stack: * ebuild.sh, line 54: Called src_install * environment, line 4832: Called die * The specific snippet of code: * doins API/html/* || die; * * If you need support, post the output of 'emerge --info =sci-chemistry/openbabel-2.2.3', * the complete build log and the output of 'emerge -pqv =sci-chemistry/openbabel-2.2.3'. * The complete build log is located at '/var/tmp/portage/sci-chemistry/openbabel-2.2.3/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/openbabel-2.2.3/temp/environment'. * S: '/var/tmp/portage/sci-chemistry/openbabel-2.2.3/work/openbabel-2.2.3' * QA Notice: file does not exist: * * doins: API/html/* does not exist The last succesful install was in december: root@moose:/root(8)# genlop -t openbabel | tail Fri Nov 6 17:57:28 2009 >>> sci-chemistry/openbabel-2.2.3 merge time: 5 minutes and 5 seconds. Tue Nov 10 13:37:48 2009 >>> sci-chemistry/openbabel-2.2.3 merge time: 4 minutes and 38 seconds. Mon Dec 7 20:37:16 2009 >>> sci-chemistry/openbabel-2.2.3 merge time: 6 minutes and 40 seconds.
Fixed in tree + 19 Jun 2010; Kacper Kowalik <xarthisius@gentoo.org> + openbabel-2.2.3.ebuild: + Fix docs install wrt bug 322543. Thanks Juergen Rose + <rose@rz.uni-potsdam.de> for reporting +
