On Sat, Aug 24, 2013 at 6:57 PM, François Bissey <fbissey@slingshot.co.nz>wrote:

> On 2013-08-24 03:30, P Purkayastha wrote:
>
>> Are you sure? They are all valid (though equery resolves the links):
>>
>> ~» equery b /usr/lib/{libcblas.so,libf77blas.so,libatlas.so}
>>  * Searching for
>> /usr/lib/libcblas.so,/usr/lib/libf77blas.so,/usr/lib/libatlas.so ...
>>  sci-libs/atlas-3.10.1-r1 (/usr/lib64/libatlas.so.3)
>> sci-libs/atlas-3.10.1-r1 (/usr/lib64/libf77blas.so.3)
>> sci-libs/gsl-1.14 (/usr/lib64/libgslcblas.so.0.0.0)
>>
>>  atlas 3.10.1 and gsl 1.14 _at_the_same_time_? You have a mix of the old
> virtual from the main tree and new libraries from the science overlay.
>
> Portage will complain (yesterday).
>
> When you decide to do the clean up be sure to post here so we can
> make sure you are back in a sane state.
>
> Francois
>
>
Portage did complain today. I had to unmask eselect::gentoo and
gsl::science. Then I upgraded and it had the following changes to show

 ~» quietemerge -uDv world $QEMERGE
--------------------------------------------------- Pretended emerge
---------------------------------------------------

These are the packages that would be merged, in order:

Calculating dependencies .. ... .. ... .. .......... done!
[ebuild U ] sys-libs/timezone-data-2013c [2013b] USE="nls" 346 kB
[ebuild U ] media-libs/tiff-4.0.3-r4 [4.0.3-r2] USE="cxx jpeg lzma zlib
-jbig -static-libs" 0 kB
[ebuild U ] dev-libs/klibc-1.5.25 [1.5.23] USE="-debug" 499 kB
[ebuild U ] dev-lang/python-2.7.5-r2:2.7 [2.7.5:2.7] USE="gdbm ncurses
readline sqlite ssl threads (wide-unicode) xml -berkdb -build -doc
-examples -hardened -ipv6 -tk -wininst" 0 kB
[ebuild UD~] app-admin/eselect-1.3.6::gentoo [1.3.7-r100::science]
USE="-doc (-emacs%) (-vim-syntax%*)" 164 kB
[ebuild U ~] sys-apps/portage-2.2.1 [2.2.0] USE="(ipc) xattr -build -doc
-epydoc (-pypy2_0) -python2 -python3 (-selinux)" LINGUAS="-ru"
PYTHON_TARGETS="python2_7 (-pypy1_9) -pypy2_0 -python2_6 (-python3_1)
-python3_2 -python3_3 (-python3_4)" 881 kB
[ebuild U ~] sci-libs/gsl-1.16-r1::science [1.14::gentoo]
USE="-cblas-external -static-libs%" 3,452 kB
[ebuild N ] app-shells/bash-completion-1.3-r2 0 kB
[ebuild U ~] media-libs/fontconfig-2.10.93:1.0 [2.10.92:1.0] USE="-doc
-static-libs" ABI_X86="(64) -32 (-x32)" 1,491 kB

Total: 9 packages (7 upgrades, 1 downgrade, 1 new), Size of downloads:
6,830 kB

WARNING: One or more updates have been skipped due to a dependency conflict:

app-admin/eselect:0

(app-admin/eselect-1.3.7-r100::science, ebuild scheduled for merge)
conflicts with
  <app-admin/eselect-1.3.7 required by
(app-shells/bash-completion-1.3-r2::gentoo, ebuild scheduled for merge)


The links are still there, so nothing got hosed till now :-)

~» equery b /usr/lib/{libcblas.so,libf77blas.so,libatlas.so}
* Searching for
/usr/lib/libcblas.so,/usr/lib/libf77blas.so,/usr/lib/libatlas.so ...
sci-libs/atlas-3.10.1-r1 (/usr/lib64/libatlas.so.3)
sci-libs/atlas-3.10.1-r1 (/usr/lib64/libf77blas.so.3)
sci-libs/gsl-1.16-r1 (/usr/lib64/libgslcblas.so.0.0.0)

Thanks for the warning, though.  I am still trying to compile sage in my
home directory though. Currently stuck at scipy since it can't find ATLAS.
:-( I will try to trouble shoot and probably mail sage-devel about this.