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-   -   emerge blas-atlas fails (http://www.linux-archive.org/gentoo-alt/286052-emerge-blas-atlas-fails.html)

Andreas Amann 11-25-2009 12:43 PM

emerge blas-atlas fails
 
Hello all,

"emerge blas-atlas" apparently wants to install stuff into /etc instead of
$EPREFIX/etc

Anybody knows how to fix this?

Here are my symptons:

Output of
>emerge blas-atlas
...
>>> Completed installing blas-atlas-3.9.3 into
>>> /local/aamann/gentoo-prefix/var/tmp/portage/sci-libs/blas-atlas-3.9.3/image/local/aamann/gentoo-prefix/

strip: x86_64-pc-linux-gnu-strip --strip-unneeded -R .comment
usr/lib/libatlas.so.0.0.0
usr/lib/blas/threaded-atlas/libblas.so.0.0.0
usr/lib/blas/threaded-atlas/libcblas.so.0.0.0
usr/lib/blas/atlas/libblas.so.0.0.0
usr/lib/blas/atlas/libcblas.so.0.0.0
usr/lib/blas/threaded-atlas/libcblas.a
usr/lib/blas/threaded-atlas/libblas.a
usr/lib/blas/atlas/libcblas.a
usr/lib/blas/atlas/libblas.a
usr/lib/libatlas.a
* QA Notice: the following files are outside of the prefix:
* /etc
* /etc/env.d
* /etc/env.d/cblas
* /etc/env.d/cblas/lib
* /etc/env.d/cblas/lib/atlas-threads
* /etc/env.d/cblas/lib/atlas
* /etc/env.d/blas
* /etc/env.d/blas/lib
* /etc/env.d/blas/lib/atlas-threads
* /etc/env.d/blas/lib/atlas
* ERROR: sci-libs/blas-atlas-3.9.3 failed:
* Aborting due to QA concerns: there are files installed outside the
prefix
*
* Call stack:
* misc-functions.sh, line 1410: Called install_qa_check
* misc-functions.sh, line 89: Called install_qa_check_prefix
* misc-functions.sh, line 589: Called die
* The specific snippet of code:
* die "Aborting due to QA concerns: there are files
installed outside the prefix"
*

Here the output of
>emerge -pqv =sci-libs/blas-atlas-3.9.3
[ebuild N ] sci-libs/blas-atlas-3.9.3 USE="-debug -doc"

and the output of
>emerge --info =sci-libs/blas-atlas-3.9.3
Portage 2.2.00.14813-prefix (prefix/linux/amd64, gcc-4.2.4, unavailable,
2.6.24.4-64.fc8 x86_64)
================================================== ===============
System Settings
================================================== ===============
System uname:
Linux-2.6.24.4-64.fc8-x86_64-AMD_Athlon-tm-_64_X2_Dual_Core_Processor_4200+-with-fedora-8-Werewolf
Timestamp of tree: Tue, 24 Nov 2009 14:02:19 +0000
app-shells/bash: 4.0_p35
dev-java/java-config: 1.3.7-r1, 2.1.7
dev-lang/python: 2.5.4-r2, 2.6.2-r2
dev-util/cmake: 2.6.2-r1
sys-apps/sandbox: 2.0
sys-devel/autoconf: 2.63-r01.1
sys-devel/automake: 1.9.6-r2, 1.10.2-r00.1, 1.11
sys-devel/binutils: 2.19.51.0.1
sys-devel/gcc-config: 1.4.0-r04.6
sys-devel/libtool: 2.2.6a-r00.2
virtual/os-headers: 2.6.30-r1
ACCEPT_KEYWORDS="~amd64-linux"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/
/etc/fonts/fonts.conf /etc/gconf /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-O2 -pipe"
DISTDIR="/local/aamann/gentoo-prefix/usr/portage/distfiles"
FEATURES="assume-digests collision-protect distlocks fixpackages news
parallel-fetch preserve-libs protect-owned sfperms strict unmerge-logs
unmerge-orphans userfetch"
GENTOO_MIRRORS="http://distfiles.gentoo.org
http://distro.ibiblio.org/pub/linux/distributions/gentoo"
LANG="en_IE.UTF-8"
LDFLAGS="-Wl,-O1"
PKGDIR="/local/aamann/gentoo-prefix/usr/portage/packages"
PORTAGE_CONFIGROOT="/local/aamann/gentoo-prefix/"
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="/local/aamann/gentoo-prefix/var/tmp"
PORTDIR="/local/aamann/gentoo-prefix/usr/portage"
SYNC="rsync://rsync.prefix.freens.org/gentoo-portage-prefix"
USE="X amd64 berkdb bzip2 cairo cli cracklib crypt cxx dri fftw fortran gdbm
iconv ipv6 latex mmx modules mudflap ncurses nls nptl nptlonly openmp pcre
pdf perl pppd prefix python readline reflection session spl sse sse2 ssl
sysfs tcpd unicode xorg zlib" 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 authn_alias authn_anon 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 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" ELIBC="glibc"
INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad
cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text"
USERLAND="GNU" VIDEO_CARDS="fbdev glint intel mach64 mga neomagic nv r128
radeon savage sis tdfx trident vesa vga via vmware voodoo"
Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK,
LC_ALL, LINGUAS, MAKEOPTS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS,
PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY

Jacob Godserv 11-25-2009 02:18 PM

emerge blas-atlas fails
 
On Wed, Nov 25, 2009 at 08:43, Andreas Amann <amann@physik.tu-berlin.de> wrote:
> Hello all,
>
> "emerge blas-atlas" apparently wants to install stuff into /etc instead of
> $EPREFIX/etc
>
> Anybody knows how to fix this?

Be sure to file a bug report.

I've encountered these /etc issues as well, so I tried to look into
this just now, but I got a warning that my gcc doesn't have fortran
support. It might be a little while, then, before I can help you, if
at all. I'll keep you posted.


--
Jacob

"For then there will be great distress, unequaled
from the beginning of the world until now — and never
to be equaled again. If those days had not been cut
short, no one would survive, but for the sake of the
elect those days will be shortened."

Are you ready?

Jeremy Olexa 11-25-2009 02:40 PM

emerge blas-atlas fails
 
On Wed, 25 Nov 2009 10:18:17 -0500, Jacob Godserv <jacobgodserv@gmail.com>
wrote:
> On Wed, Nov 25, 2009 at 08:43, Andreas Amann <amann@physik.tu-berlin.de>
> wrote:
>> Hello all,
>>
>> "emerge blas-atlas" apparently wants to install stuff into /etc instead
>> of
>> $EPREFIX/etc
>>
>> Anybody knows how to fix this?
>
> Be sure to file a bug report.
>
> I've encountered these /etc issues as well, so I tried to look into
> this just now, but I got a warning that my gcc doesn't have fortran
> support. It might be a little while, then, before I can help you, if
> at all. I'll keep you posted.

The ebuild and package are quite difficult (like all sci packages). A
homebrew'd configure script and no way to change the path for config files.
Not sure what needs to be done really. Probably best to see the first
version that worked and what changed. At some point, everything that was
added to the prefix tree was tested. New versions after were not explicitly
tested when they were added to the tree. We rely on bug reports and people
helping to fix issues. :)

Thanks,
-Jeremy

Andreas Amann 11-25-2009 06:08 PM

emerge blas-atlas fails
 
> The ebuild and package are quite difficult (like all sci packages). A
> homebrew'd configure script and no way to change the path for config files.
> Not sure what needs to be done really. Probably best to see the first
> version that worked and what changed. At some point, everything that was
> added to the prefix tree was tested. New versions after were not explicitly
> tested when they were added to the tree. We rely on bug reports and people
> helping to fix issues. :)
>

Fair enough. Here my go in trying to at least localise the problem (Keep in
mind that I have no general knowledge of gentoo, other than running
gentoo-prefix.)

I notice that the lines

eselect blas add $(get_libdir) "${FILESDIR}"/eselect.blas.atlas ${ESELECT_PROF}
eselect cblas add $(get_libdir) "${FILESDIR}"/eselect.cblas.atlas ${ESELECT_PROF}

in blas-atlas-3.9.3.ebuild are apparently responsible for the problem.
Expanding the variables the first one translates to
eselect blas add lib $EPREFIX/usr/portage/sci-libs/blas-atlas/files/eselect.blas.atlas atlas

now the interesting thing is that when I execute this line from the
commandline, then indeed it does the right thing, and basically copies
$EPREFIX/usr/portage/sci-libs/blas-atlas/files/eselect.blas.atlas
to
$EPREFIX/etc/env.d/blas/lib/atlas

(The file eselect.blas.atlas does itself not look very prefix friendly, but
this is a different issue.)

however when this line is executed during "emerge blas-atlas", then there
seems to be some mechanism, which installs all files first to a temporary
tree under $EPREFIX/var/tmp/portage/sci-libs/blas-atlas-3.9.3/image/
Here is obviosly, where the error occurs, since the above eselect writes
into $EPREFIX/var/tmp/portage/sci-libs/blas-atlas-3.9.3/image/etc/
instead of
$EPREFIX/var/tmp/portage/sci-libs/blas-atlas-3.9.3/image/$EPREFIX/etc/

then the function install_qa_check_prefix() which is located in
$EPREFIX/usr/lib/portage/bin/misc-functions.sh
notices that there are files to be installed outside $EPREFIX and barfs out.

So far so good. What I do however not know, is why "eselect" misbehaves when
called from within emerge.

I have now filed a bug for this, it is at
https://bugs.gentoo.org/show_bug.cgi?id=294606

So from my limited understanding this could well be a bug which is not
directly due to the ebuild (which seem to be a couple of months old), but
possibly due to eselect not doing the right thing when called from within
emerge. Was there any recent change in the eselect infrastructure that could
have triggered this?

Andreas

Michael Yang 11-25-2009 06:18 PM

emerge blas-atlas fails
 
> then the function install_qa_check_prefix() which is located in
> $EPREFIX/usr/lib/portage/bin/misc-functions.sh
> notices that there are files to be installed outside $EPREFIX and barfs out.
>
> So far so good. What I do however not know, is why "eselect" misbehaves when
> called from within emerge.
>
> I have now filed a bug for this, it is at
> https://bugs.gentoo.org/show_bug.cgi?id=294606

I think #277849 will provide some helpful information to help this
along, as the same type of install_qa_check_prefix() problems were
fixed with blas-reference without having to change the ebuild script
much.

Andreas Amann 11-25-2009 09:54 PM

emerge blas-atlas fails
 
On Wed, Nov 25, 2009 at 02:18:02PM -0500, Michael Yang wrote:
> > then the function install_qa_check_prefix() which is located in
> > $EPREFIX/usr/lib/portage/bin/misc-functions.sh
> > notices that there are files to be installed outside $EPREFIX and barfs out.
> >
> > So far so good. What I do however not know, is why "eselect" misbehaves when
> > called from within emerge.
> >
> > I have now filed a bug for this, it is at
> > https://bugs.gentoo.org/show_bug.cgi?id=294606
>
> I think #277849 will provide some helpful information to help this
> along, as the same type of install_qa_check_prefix() problems were
> fixed with blas-reference without having to change the ebuild script
> much.
>


Thanks a lot for this pointer!
"emerge eselect" solved my problem.

Andreas


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