'emerge -vD unison' fails with: root@caiman:/root(36)# emerge -vD unison These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild R ] net-misc/unison-2.32.52 USE="doc ocamlopt threads -debug -gtk* -static -test" 0 kB Total: 1 package (1 reinstall), Size of downloads: 0 kB >>> Verifying ebuild manifests >>> Emerging (1 of 1) net-misc/unison-2.32.52 >>> Failed to emerge net-misc/unison-2.32.52, Log file: >>> '/var/tmp/portage/net-misc/unison-2.32.52/temp/build.log' >>> Jobs: 0 of 1 complete, 1 failed Load avg: 0.39, 0.48, 0.52 * Package: net-misc/unison-2.32.52 * Repository: gentoo * Maintainer: ml@gentoo.org * USE: amd64 doc elibc_glibc kernel_linux multilib ocamlopt threads userland_GNU * FEATURES: sandbox >>> Unpacking source... >>> Unpacking unison-2.32.52.tar.gz to /var/tmp/portage/net-misc/unison-2.32.52/work >>> Unpacking unison-2.32.52-manual.pdf to /var/tmp/portage/net-misc/unison-2.32.52/work unpack unison-2.32.52-manual.pdf: file format not recognized. Ignoring. >>> Unpacking unison-2.32.52-manual.html to /var/tmp/portage/net-misc/unison-2.32.52/work unpack unison-2.32.52-manual.html: file format not recognized. Ignoring. >>> Source unpacked in /var/tmp/portage/net-misc/unison-2.32.52/work >>> Preparing source in /var/tmp/portage/net-misc/unison-2.32.52/work/unison-2.32.52 ... * Applying unison-2.27.57-as-needed.patch ... [ ok ] * Applying unison-mymap.patch ... [ ok ] >>> Source prepared. >>> Configuring source in /var/tmp/portage/net-misc/unison-2.32.52/work/unison-2.32.52 ... >>> Source configured. >>> Compiling source in /var/tmp/portage/net-misc/unison-2.32.52/work/unison-2.32.52 ... make -j7 THREADS=true UISTYLE=text CFLAGS= buildexecutable ... ocamlopt -I lwt -I ubase -c /var/tmp/portage/net-misc/unison-2.32.52/work/unison-2.32.52/fingerprint.mli File "/var/tmp/portage/net-misc/unison-2.32.52/work/unison-2.32.52/lwt/lwt_unix.ml", line 294, characters 12-59: Warning 21: this statement never returns (or has an unsound type.) File "/var/tmp/portage/net-misc/unison-2.32.52/work/unison-2.32.52/lwt/lwt_unix.ml", line 394, characters 10-57: Warning 21: this statement never returns (or has an unsound type.) ocamlopt: osx.mli ---> osx.cmi ocamlopt -I lwt -I ubase -c /var/tmp/portage/net-misc/unison-2.32.52/work/unison-2.32.52/osx.mli File "/var/tmp/portage/net-misc/unison-2.32.52/work/unison-2.32.52/lwt/lwt_unix.ml", line 437, characters 10-62: Warning 21: this statement never returns (or has an unsound type.) ocamlopt: props.mli ---> props.cmi ocamlopt -I lwt -I ubase -c /var/tmp/portage/net-misc/unison-2.32.52/work/unison-2.32.52/props.mli ocamlopt: fileinfo.mli ---> fileinfo.cmi ... ocamlopt -I lwt -I ubase -c /var/tmp/portage/net-misc/unison-2.32.52/work/unison-2.32.52/linktext.ml Linking unison ocamlopt -verbose -I lwt -I ubase -o unison unix.cmxa str.cmxa bigarray.cmxa ubase/projectInfo.cmx ubase/myMap.cmx ubase/safelist.cmx ubase/uprintf.cmx ubase/util.cmx ubase/rx.cmx ubase/uarg.cmx ubase/prefs.cmx ubase/trace.cmx lwt/pqueue.cmx lwt/lwt.cmx lwt/lwt_util.cmx lwt/lwt_unix.cmx bytearray.cmx case.cmx pred.cmx uutil.cmx fileutil.cmx name.cmx path.cmx fspath.cmx fingerprint.cmx abort.cmx osx.cmx external.cmx props.cmx fileinfo.cmx os.cmx lock.cmx clroot.cmx common.cmx tree.cmx checksum.cmx terminal.cmx transfer.cmx xferhint.cmx remote.cmx globals.cmx copy.cmx stasher.cmx update.cmx files.cmx sortri.cmx recon.cmx transport.cmx strings.cmx uicommon.cmx uitext.cmx test.cmx main.cmx linktext.cmx osxsupport.o pty.o bytearray_stubs.o /usr/lib64 -cclib -lutil /usr/bin/ocamlopt: don't know what to do with /usr/lib64. Usage: ocamlopt <options> <files> Options are: -fPIC Generate position-independent machine code (default) -fno-PIC Generate position-dependent machine code -a Build a library -annot Save information in <filename>.annot -c Compile only (do not link) ... -help Display this list of options --help Display this list of options make: *** [unison] Error 2 emake failed Reproducible: Always root@caiman:/root(37)# emerge --info =net-misc/unison-2.32.52 Portage 2.1.10.38 (default/linux/amd64/10.0, gcc-4.5.3, glibc-2.14.1-r0, 3.1.1-gentoo x86_64) ================================================================= System Settings ================================================================= System uname: Linux-3.1.1-gentoo-x86_64-AMD_Phenom-tm-_II_X6_1090T_Processor-with-gentoo-2.1 Timestamp of tree: Sat, 26 Nov 2011 15:30:01 +0000 app-shells/bash: 4.2_p20 dev-java/java-config: 2.1.11-r3 dev-lang/python: 2.7.2-r3::sage-on-gentoo, 3.2.2 dev-util/cmake: 2.8.6-r4 dev-util/pkgconfig: 0.26 sys-apps/baselayout: 2.1 sys-apps/openrc: 0.9.6 sys-apps/sandbox: 2.5 sys-devel/autoconf: 2.13, 2.68 sys-devel/automake: 1.9.6-r3, 1.10.3, 1.11.1-r1 sys-devel/binutils: 2.22 sys-devel/gcc: 4.5.3-r1 sys-devel/gcc-config: 1.5-r2 sys-devel/libtool: 2.4.2 sys-devel/make: 3.82-r3 sys-kernel/linux-headers: 2.6.39 (virtual/os-headers) sys-libs/glibc: 2.14.1 Repositories: gentoo x11 bicatali science sage-on-gentoo java-overlay sunrise x-portage x-cpan x-g-octave ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA PUEL dlj-1.1 skype-eula googleearth AdobeFlash-10.1 cadsoft Oracle-BCLA-JavaSE" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=amdfam10 -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.0/conf /usr/share/openvpn/easy-rsa /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.3/ext-active/ /etc/php/apache2-php5.4/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cgi-php5.4/ext-active/ /etc/php/cli-php5.3/ext-active/ /etc/php/cli-php5.4/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=amdfam10 -O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests binpkg-logs distlocks ebuild-locks fixlafiles news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch" FFLAGS="" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_US.UTF-8" LC_ALL="C" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="de fr" MAKEOPTS="-j7" 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/x11 /var/lib/layman/bicatali /var/lib/layman/science /var/lib/layman/sage-on-gentoo /var/lib/layman/java-overlay /var/lib/layman/sunrise /usr/local/portage /var/lib/cpan /var/lib/g-octave" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="3dnow 3dnowext 64bit R X Xaw3d a52 aac abiword acl acpi admin afs alsa amd64 amrr ao apache2 applet archive arpack asf aspell assistant atlas audacious audiofile automap automount bash-completion berkdb blas blast bluetooth boo boost 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 declarative designer devhelp device-mapper dga dia djvu doc dri ds2490 ds9097 ds9097u dv dvb dvd dvdr dvi dynamicplugin eds elf emacs emboss emf encode epiphany evo examples exif expat extensions extra extras fame ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpx fts3 fuse galago gcj gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp ginac git glade glib glpk gml gmp gmtsuppl gnome gnome-keyring gnome-print gnuplot gnutls gphoto2 gpm grammar graphics graphtft graphviz grass gs gsl gsm gstreamer gtk gudev guile harness hddtemp hdf hdf5 hdri http httpd hvm hwdb iconv icq icu id3 imagemagick imap innodb inotify ipod ipv6 irda ithreads jabber jadetex java java6 jbig john jpeg jpeg2k kdrive kerberos kpathsea kqemu kvm ladspa lame lapack latex latex3 lcms ldap lensfun libffi libgda libnotify libsamplerate lm_sensors lua lzo mad mail maildir mapnik math matroska mkl mmx mmxext mng modules mono moonlight motif mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap multilib musicbrainz mysql mysqli nautilus ncurses netcdf netpbm network networking networkmanager nfs nls nntp nptl nptlonly nsplugin ntfs ntp numpy obex objc ocr octave odbc ogdi ogg ole openexr opengl openmp overview pam pcre pda pdf perl plotutils plugins png podcast policykit portaudio posix postgres postscript ppds pppd preview-latex proj projectx pstricks pulseaudio python python-bindings q16 q32 qemu qhull qt3support qt4 quicktime readline reiserfs reports rle romio rpc rrdcgi rrdtool sage samba sasl science sdk sdl secure-delete semantic-desktop server session sip slang slp smbclient smp sms sndfile snmp soup sox speex spell sql sqlite sse sse2 sse4a ssl stlport subtitles subversion suexec svg svm swig sysfs szip t1lib tcl tcpd tex tex4ht texmacs tgif theora threads thunderbird tidy tiff tk tools truetype udev unicode usb userlocales utempter v4l2 vaapi video virtualbox vorbis wav webdav webdav-serf webkit wmf wxwidgets xattr xcb xemacs xext xft xine xml xmlreader xmlrpc xorg xpm xulrunner xv xvid xvmc yaml zlib zvbi" 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" 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 cgid 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" CALLIGRA_FEATURES="kexi words flow plan stage tables krita karbon braindump" CAMERAS="canon" 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 ubx" 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" PHP_TARGETS="php5-3" QEMU_SOFTMMU_TARGETS="i386 ppc ppc64 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="radeon vesa" 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, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS ================================================================= Package Settings ================================================================= net-misc/unison-2.32.52 was built with the following: USE="doc gtk (multilib) ocamlopt threads -debug -static -test"
Created attachment 293859 [details] /var/tmp/portage/net-misc/unison-2.32.52/temp/build.log
I reemerged dev-lang/ocaml, lablgl and lablgtk with the following USE flags: root@moose:/root(21)# emerge -pvD lablgl lablgtk dev-lang/ocaml These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild R ] dev-lang/ocaml-3.12.1 USE="X emacs gdbm latex ncurses ocamlopt tk xemacs" 0 kB [ebuild R ] dev-ml/lablgl-1.04 USE="doc ocamlopt tk -glut" 0 kB [ebuild R ] dev-ml/lablgtk-2.14.2 USE="examples glade ocamlopt opengl spell svg -debug -gnome -gnomecanvas -sourceview" 0 kB But 'emerge unison' still fails with: ocamlopt -verbose -I lwt -I ubase -I +lablgtk2 -o unison unix.cmxa str.cmxa bigarray.cmxa lablgtk.cmxa ubase/projectInfo.cmx ubase/myMap.cmx ubase/safelist.cmx ubase/uprintf.cmx ubase/util.cmx ubase/rx.cmx ubase/uarg.cmx ubase/prefs.cmx ubase/trace.cmx lwt/pqueue.cmx lwt/lwt.cmx lwt/lwt_util.cmx lwt/lwt_unix.cmx bytearray.cmx case.cmx pred.cmx uutil.cmx fileutil.cmx name.cmx path.cmx fspath.cmx fingerprint.cmx abort.cmx osx.cmx external.cmx props.cmx fileinfo.cmx os.cmx lock.cmx clroot.cmx common.cmx tree.cmx checksum.cmx terminal.cmx transfer.cmx xferhint.cmx remote.cmx globals.cmx copy.cmx stasher.cmx update.cmx files.cmx sortri.cmx recon.cmx transport.cmx strings.cmx uicommon.cmx uitext.cmx test.cmx main.cmx pixmaps.cmx uigtk2.cmx linkgtk2.cmx osxsupport.o pty.o bytearray_stubs.o /usr/lib64 -cclib -lutil /usr/bin/ocamlopt: don't know what to do with /usr/lib64. I checked that this /usr/lib64 comes from the CLIBS macro in Makefile.OCaml, which sets under UNIX conditions: CLIBS+=-cclib -lutil But CLIBS seems to be someway defined at x86_64 as /usr/lib64 rose@lynx:/home/rose(23)$ uname -a Linux lynx 3.1.3-gentoo #1 SMP Mon Nov 28 14:25:12 CET 2011 x86_64 Intel(R) Core(TM)2 Duo CPU T8300 @ 2.40GHz GenuineIntel GNU/Linux rose@lynx:/home/rose(24)$ env | grep CLIBS CLIBS=/usr/lib64 Thus after unsetting CLIBS I was able to emerge unison: root@moose:/var/tmp/portage/net-misc/unison-2.32.52/work/unison-2.32.52(30)# unset CLIBS root@moose:/var/tmp/portage/net-misc/unison-2.32.52/work/unison-2.32.52(31)# emerge -v unison These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild N ] net-misc/unison-2.32.52 USE="doc gtk ocamlopt threads -debug -static -test" 0 kB Total: 1 package (1 new), Size of downloads: 0 kB >>> Verifying ebuild manifests >>> Emerging (1 of 1) net-misc/unison-2.32.52 >>> Installing (1 of 1) net-misc/unison-2.32.52 >>> Recording net-misc/unison in "world" favorites file... >>> Jobs: 1 of 1 complete Load avg: 0.21, 0.06, 0.45 >>> Auto-cleaning packages... >>> No outdated packages were found on your system. * GNU info directory index is up-to-date.
It seems that again sci-libs/ccp4-libs-6.1.3-r10 is responsible for setting of CLIB and CLIPS. These macros are set in /etc/profile.d/40ccp4.setup.csh which is installed by ccp4-libs: root@moose:/root(38)# qfile -v /etc/profile.d/40ccp4.setup.sh sci-libs/ccp4-libs-6.1.3-r10 (/etc/profile.d/40ccp4.setup.sh)
During a new gentoo installation I hit this error again. I have a file /etc/profile.d/40ccp4.setup.sh which exports CLIB=/usr/lib64 and CLIBS=/usr/lib64. But ccp4-libs are not installed, I don't know where from this file comes: root@leopard:/usr/local/portage/dev-scheme/guile-gnome-platform(227)# qfile -v 40ccp4.setup.sh root@leopard:/usr/local/portage/dev-scheme/guile-gnome-platform(228)# grep CLIB /etc/profile.d/*.sh /etc/profile.d/40ccp4.setup.sh:# etc. Non-shareable files reside in $CBIN and $CLIB (see below). /etc/profile.d/40ccp4.setup.sh:# CLIB: location of (binary) library files such as libccp4.a and libccp4.so; /etc/profile.d/40ccp4.setup.sh: export CLIB=/usr/lib64 /etc/profile.d/40ccp4.setup.sh:# so on multiple installs it need to be unique and not in $CLIBD /etc/profile.d/40ccp4.setup.sh:export MMCIFDIC=$CLIB/cif_mmdic.lib /etc/profile.d/40ccp4.setup.sh:# They are distributed with CCP4 in $CLIBD. This env must have the trailing \ or / /etc/profile.d/40ccp4.setup.sh:### CLIBD_MON Point to the location of the dictionary files for REFMAC5 /etc/profile.d/40ccp4.setup.sh:# They are distributed with CCP4 in $CLIBD/monomers. This env must have /etc/profile.d/40ccp4.setup.sh:export CLIBD_MON=/usr/share/ccp4/data/monomers/ /etc/profile.d/40ccp4.setup.sh:export PUBLIC_FONT84=$CLIB/font84.dat # plot84 fonts [used by plot84lib] /etc/profile.d/40ccp4.setup.sh: export CLIBD=/usr/share/ccp4/data /etc/profile.d/40ccp4.setup.sh: export CLIBS=/usr/lib64 On a second system this file is installed by ccp4-libs-6.1.3-r11. 'emerge unison' there also does not work. Linking unison ocamlopt -verbose -I lwt -I ubase -I +lablgtk2 -o unison unix.cmxa str.cmxa bigarray.cmxa lablgtk.cmxa ubase/projectInfo.cmx ubase/myMap.cmx ubase/safelist.cmx ubase/uprintf.cmx ubase/util.cmx ubase/rx.cmx ubase/uarg.cmx ubase/prefs.cmx ubase/trace.cmx lwt/pqueue.cmx lwt/lwt.cmx lwt/lwt_util.cmx lwt/lwt_unix.cmx bytearray.cmx case.cmx pred.cmx uutil.cmx fileutil.cmx name.cmx path.cmx fspath.cmx fingerprint.cmx abort.cmx osx.cmx external.cmx props.cmx fileinfo.cmx os.cmx lock.cmx clroot.cmx common.cmx tree.cmx checksum.cmx terminal.cmx transfer.cmx xferhint.cmx remote.cmx globals.cmx copy.cmx stasher.cmx update.cmx files.cmx sortri.cmx recon.cmx transport.cmx strings.cmx uicommon.cmx uitext.cmx test.cmx main.cmx pixmaps.cmx uigtk2.cmx linkgtk2.cmx osxsupport.o pty.o bytearray_stubs.o /usr/lib64 -cclib -lutil /usr/bin/ocamlopt: don't know what to do with /usr/lib64. ... Usage: ocamlopt <options> <files> Options are: -fPIC Generate position-independent machine code (default) ... --help Display this list of options make: *** [unison] Error 2 emake failed root@moose:/root(10)# qfile -v 40ccp4.setup.sh sci-libs/ccp4-libs-6.1.3-r11 (/etc/profile.d/40ccp4.setup.sh)
Hmmm, scientists are customed to misuse env variables. Ccing jlec, maintainer of sci-libs/ccp4-libs to look into this.
I try to drop that from ccp4
Is this still valid today? :/
*** Bug 464098 has been marked as a duplicate of this bug. ***
