Bugzilla Bug 175630

It does not matter of the version (6.0.1 or 6.02) but ccp4 is unable to be
properly built and installed. 






Reproducible: Always

Steps to Reproduce:
1. emerge ccp4
2.
3.

Actual Results:  
 * Calling dosym libxdl_view.so.2.0.0 /usr/lib/ libxdl_view.so .2
 * Calling dosym libxdl_view.so.2.0.0 /usr/lib/ libxdl_view.so .2.2
 * Calling dosym libxdl_view.so.2.0.0 /usr/lib/ libxdl_view.so 
doexe: warning, skipping directory
/var/tmp/portage/sci-chemistry/ccp4-6.0.2/work/ccp4-6.0.2/ccp4i/bin/UNIX
doexe: warning, skipping directory
/var/tmp/portage/sci-chemistry/ccp4-6.0.2/work/ccp4-6.0.2/ccp4i/bin/WINDOWS
install: cannot stat
`/var/tmp/portage/sci-chemistry/ccp4-6.0.2/work/ccp4-6.0.2/include/clipper': No
such file or directory

!!! ERROR: sci-chemistry/ccp4-6.0.2 failed.
Call stack:
  ebuild.sh, line 1614:   Called dyn_install
  ebuild.sh, line 1060:   Called qa_call 'src_install'
  environment, line 3939:   Called src_install
  ccp4-6.0.2.ebuild, line 340:   Called die

!!! (no error message)
!!! 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/ccp4-6.0.2/temp/build.log'.



My emerge info: 

Portage 2.1.2.2 (default-linux/x86/2006.1, gcc-4.1.1, glibc-2.5-r0,
2.6.20-gentoo-r6 i686)
=================================================================
System uname: 2.6.20-gentoo-r6 i686 Intel(R) Pentium(R) 4 CPU 3.06GHz
Gentoo Base System release 1.12.9
Timestamp of tree: Thu, 19 Apr 2007 04:20:01 +0000
ccache version 2.4 [enabled]
dev-java/java-config: 1.3.7, 2.0.31-r5
dev-lang/python:     2.4.3-r4
dev-python/pycrypto: 2.0.1-r5
dev-util/ccache:     2.4-r6
sys-apps/sandbox:    1.2.17
sys-devel/autoconf:  2.13, 2.61
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
sys-devel/binutils:  2.16.1-r3
sys-devel/gcc-config: 1.3.15-r1
sys-devel/libtool:   1.5.22
virtual/os-headers:  2.6.17-r2
ACCEPT_KEYWORDS="x86"
AUTOCLEAN="yes"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-march=pentium4 -Os -fomit-frame-pointer -pipe"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config
/usr/kde/3.5/shutdown /usr/share/X11/xkb /usr/share/config"
CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/gconf
/etc/java-config/vms/ /etc/php/apache1-php5/ext-active/
/etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/
/etc/php/cli-php5/ext-active/ /etc/terminfo"
CXXFLAGS="-march=pentium4 -Os -fomit-frame-pointer -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="ccache distlocks metadata-transfer parallel-fetch sandbox sfperms
strict"
GENTOO_MIRRORS="ftp://ftp.ussg.iu.edu/pub/linux/gentoo
ftp://ftp.gtlib.cc.gatech.edu/pub/gentoo http://gentoo.mirrors.pair.com/
http://distfiles.gentoo.org
http://www.ibiblio.org/pub/Linux/distributions/gentoo"
LDFLAGS="-Wl,-O1"
LINGUAS="en en_US"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress
--force --whole-file --delete --delete-after --stats --timeout=180
--exclude=/distfiles --exclude=/local --exclude=/packages
--filter=H_**/files/digest-*"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage"
SYNC="rsync://rsync.namerica.gentoo.org/gentoo-portage"
USE="X aac acpi aiglx alsa amarok amr apache2 asf automount bcp beagle berkdb
binfilter bitmap-fonts bittorrent bjam boost branding bzip2 cairo caps ccache
cddb cdparanoia cdr cdrom cli cracklib crypt cups curl dba dbus divx divx4linux
dri dts dvd dvdr dvdread eds emboss emerald encode esd fam fat festival ffmpeg
fftw firefox flac flash font-server fontconfig foomaticdb fortran gaim gd gdbm
gif gimp glade glib glitz gmedia gnome gnome-print gnomecanvas gnomedb gnuplot
gnutls gphoto2 gpm grammar graphicsmagick gstreamer gtk gtk2 gtkspell gzip hal
iconv icu imagemagick ipv6 isdnlog java java5 javascript jpeg kde
kdeenablefinal kdexdeltas kerberos keyring lame latex ldap libg++ libnotify
libvisual live lm_sensors logitech-mouse logrotate mad math midi mjpeg mmx
mmxext mono mozbranding moznopango mozsvg mp3 mp4 mpeg mpeg2 mplayer
musicbrainz mysql mythtv nautilus ncurses net nfs nls nntp nptl nptlonly
nsplugin ntfs ntp nvidia nvram octave ogg on-the-fly-crypt openexr opengl
openssl oscar oss ots pam pango pcre pdf perl php plugin pmount png povray ppds
pppd pymol pyste python qt3 qt4 quicktime rar readline real reflection reiserfs
rhythmbox rtc samba sensord session sound sounds speech speedo speex spell spl
sqlite sse sse-filters sse2 ssl stream svg svga symlink sysfs syslog t1lib
tagwriting tcpd text texteffect textures themes theora thesaurus threads
threadsafe thumbnail thunderbird tidy tiff timidity tk truetype truetype-fonts
type1-fonts unicode unzip usb v4l v4l2 vcd vesa vfat videos vim visualization
vnc vncviewer voice vorbis win32codecs wma wmf wmp wordperfect x264 x86 xanim
xcomposite xforms xfs xft xine xml xorg xrandr xscreensaver xsettings xsl xslt
xterm xv xvid xvmc zip zlib zvbi" ALSA_CARDS="intel8x0 bt87x"
ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file
hooks iec958 ioplug ladspa lfloat linear meter mulaw multi null plug rate route
share shm softvol" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev joystick"
KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001
mtxorb ncurses text" LINGUAS="en en_US" USERLAND="GNU" VIDEO_CARDS="nv nvidia
vesa v4l"
Unset:  CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL,
PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

I'm also experiencing this on ~amd64 after replacing IDATE with UIDATE for
compatibility with gcc-4.1.2.  After applying the patch attached below, I get
to this exact state.  It appears as though the ebuild is trying to doinst,
doman, and possibly other things on files which do not exist in the source
folder.  I'm trying to change these lines to point to the correct locations but
I'm mostly just guess and checking.  If I find a fix before the bug is
addressed, I'll post the ebuild.  

Created an attachment (id=118005) [edit]
patch for idate incompatibility with gcc-4.1.2 in sci-chemistry/ccp4-6.0.2

(In reply to comment #2)
> Created an attachment (id=118005) [edit]
> patch for idate incompatibility with gcc-4.1.2 in sci-chemistry/ccp4-6.0.2
> 

I have compiled ccp4 from the source myself and applied that uidate patch and
it works under x86 and amd64. I'm looking into the clipper problem with the
ebuild. My guess is that there is some typo in the ebuild and puts the clipper
files in the wrong place or something related to that. 

(In reply to comment #3)
> My guess is that there is some typo in the ebuild and puts the clipper
> files in the wrong place or something related to that. 

I think this can be worked around in several ways.  One way is to remove
clipper and ssm from the for-loop which does the "doins -r ${S}/include/${i}". 
Another is to do "make install" instead of "emake install".

But I guess the proper fix would be to fix the autotooling completely.

I thing I have the solution now!

It seems that the src_install script in the ebuild copies all the files in the
.../work/ccp4-6.0.2/include into .../image/usr/include . Once it is done, the
copied files are deleted. The problem stems from the ebuild defining this
process twice and this is where it fails. In addition to clipper, the ebuild
does the same with mmdb and ssm. Surprisingly ccp4 does not suffer from this
problem. 

The fix is simply replace:
for i in ccp4 clipper mmdb ssm; do
with:
for i in ccp4 ; do

I will try to make a patch, but I am not sure how to do that yet. Until then
here is the solution and if you could beat me to making the patch, that would
be great too.

Johan Hattne, you beat me to the solution. I guess for our purposes, the work
around is ok because it works. In the end though I think you are right and the
autotooling needs to be fixed.

It is getting a little late for me and starring at this screen is making me
make a few mistakes.

Forget what I said about mmdb.

The fix is simply replace:
for i in ccp4 clipper mmdb ssm; do
with:
for i in ccp4 mmdb ; do

Donnie, 

Since you did most of the initial work on the ebuild
would you be able to advice on how to best proceed.
This a fairly complex build and I don't know
the package at all so I'd rather not break it ;)

Thanks,
Markus

Yeah, I've had this on my list for a while. It's just a pain to work on because
a big chunk of it is Fortran so ccache doesn't help at all and it takes hours
to build. Plus 6.0.1 works fine, afaik.

Fixed in 6.0.2-r1, thanks for your patience!