configure: creating ./config.status config.status: creating Makefile config.status: executing depfiles commands ------------- End Processing PropKa Configure Options ----------- checking for--disable-pdb2pka... no ------------- Begin Processing pdb2pka Configure Options ----------- checking whether you defined Numeric or Numpy... checking whether you defined numpy... yes ------------- End Processing pdb2ka Configure Options ----------- Missing ZSI !!! Please attach the following file when seeking support: !!! /var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/config.log * * ERROR: sci-chemistry/pdb2pqr-1.4.0-r1 failed. * Call stack: * ebuild.sh, line 49: Called src_compile * environment, line 3514: Called econf '--without-opal' * ebuild.sh, line 534: Called die * The specific snippet of code: * die "econf failed" * The die message: * econf failed * * If you need support, post the topmost build error, and the call stack if relevant. * A complete build log is located at '/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/temp/environment'. # emerge --info Portage 2.1.6.13 (default/linux/x86/2008.0/desktop, gcc-4.3.3, glibc-2.10.1-r0, 2.6.29.3 i686) ================================================================= System uname: Linux-2.6.29.3-i686-Mobile_Intel-R-_Pentium-R-_4_-_M_CPU_1.80GHz-with-gentoo-2.0.1 Timestamp of tree: Mon, 13 Jul 2009 09:45:02 +0000 distcc 3.1 i686-pc-linux-gnu [disabled] app-shells/bash: 4.0_p24 dev-java/java-config: 1.3.7-r1, 2.1.8-r1 dev-lang/python: 2.5.4-r3, 2.6.2-r1 dev-python/pycrypto: 2.0.1-r8 dev-util/cmake: 2.6.4 sys-apps/baselayout: 2.0.1 sys-apps/openrc: 0.4.3-r3 sys-apps/sandbox: 2.0 sys-devel/autoconf: 2.13, 2.63-r1 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 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 ACCEPT_KEYWORDS="x86 ~x86" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -march=pentium4 -mmmx -msse -msse2 -pipe -fno-strict-aliasing -ggdb" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /var/bind /var/qmail/alias /var/qmail/control /var/vpopmail/etc" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /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="-O2 -march=pentium4 -mmmx -msse -msse2 -pipe -fno-strict-aliasing -ggdb" DISTDIR="/usr/portage/distfiles" FEATURES="distlocks fixpackages metadata-transfer nostrip parallel-fetch protect-owned sandbox sfperms splitdebug strict unmerge-orphans userfetch" GENTOO_MIRRORS="http://gentoo.mirror.web4u.cz" LDFLAGS="-Wl,-O1" LINGUAS="en cs cz" 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/science /usr/local/portage/layman/sunrise /usr/local/portage/layman/java-overlay /usr/local/portage /usr/local/java-experimental /usr/local/portage/layman/java-overlay" SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage" USE="7zip R X Xaw3d a52 aac aalib ace acl acpi alsa amr amrnb amrwb apache audacious audiofile bash-completion bcmath berkdb blas bluetooth boost branding bzip2 cairo cblas cddb cdparanoia cdr clamav cli colordiff compress cpio cracklib crypt cscope css ctype cups curl curlwrappers cxx dbi dbus dga dia directfb djbfft dri dts dv dvb dvd dvdr dvdread eds emacs emboss emf enblend encode enscript exif expat fam fame fat fbcon ffmpeg fftw firefox flac flash foomaticdb fortran fpx ftp gcj gd gdbm ggi gif gimp gimpprint glibc-compat20 glibc-omitfp glut gmp gnuplot gnutls gpgme gphoto2 gpm graphviz gs gsl gsm gstreamer gtk gtkhtml hal hdf hdf5 hp2xx i8x0 icc iconv icu id3 ieee1394 ifc imagemagick imlib inifile innodb isdnlog ithreads jack java javascript jbig jce jikes jpeg jpeg2k kdtree kerberos lame lapack laptop lcms leim libcaca libedit libnotify libwww live lzo lzw mad maildir matroska mhash midi mikmod mime ming mjpeg mmap mmx mng mod_python modperl modplug motif mozilla moznoirc mp2 mp3 mp4 mpeg mpi mpi_njtree mpich2 mplayer mudflap mule musepack mxdatetime mysql mysqli ncurses netcdf netpbm network nls nntp nptl nptlonly nsplugin ntfs numeric ogg opengl openmp pam pango pcmcia pcntl pcre pdf perl plotutils plugin png pnm postproc postscript ppds pppd procmail pymol python qt3 qt3support qt4 quicktime rar raw readline recode reflection reiserfs rpm samba sasl scanner scp seamonkey server session sftp sift slp smime sndfile soap sockets spell spl sqlite srt sse sse2 ssl startup-notification subtitles subversion svg svgz sysfs sysvipc t1lib tcl tcpd tetex theora threads tidy tiff tk transcode truetype unicode urandom usb userlocales utils uuencode v4l v4l2 vcd vhook vim-syntax vim-with-x vorbis wifi win32codecs wmf wxwindows x264 x86 xanim xcf xfs xft xinerama xinetd xml xorg xpm xsl xslt xulrunner xv xvid xvmc yv12 zip zlib" ALSA_CARDS="intel-8x0m" 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 dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info log_config mem_cache mime mime_magic rewrite setenvif speling status unique_id userdir usertrack vhost_alias negotiation" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en cs cz" USERLAND="GNU" VIDEO_CARDS="radeon vesa" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LANG, LC_ALL, MAKEOPTS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Created attachment 198349 [details] build.log
Missing ZSI !!! Please attach the following file when seeking support: !!! /var/tmp/portage/sci-chemistry/pdb2pqr-1.4.0-r1/work/pdb2pqr-1.4.0/config.log
Created attachment 198360 [details] config.log
econf was called with --without-opal and ebuild has opal? ( dev-python/zsi ) so dev-python/zsi didn't get pulled in.., the flag doesn't work?
Created attachment 204293 [details, diff] adding epatch to ebuild
Created attachment 204294 [details, diff] using --without-val sets $with_val to "no" _not_ to ""
(In reply to comment #6) > Created an attachment (id=204294) [edit] > using --without-val sets $with_val to "no" _not_ to "" > Thanks a lot for the patch. I've added this to our existing patch and --without-opal seems to work now. Best, Markus