ferreirafm | 17 Oct 15:52 2014
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science not syncing

Hi Gentoo Scientists,
I'm frequently getting the following error when syncing science overlay.
Is git.overlay.gentoo.org dead?
Best,
Fred



####################### 
receiving file list ... 
 100 files...
... 
...
 62600 files...
 62700 files...
                    
sent 76 bytes  received 1,480,180 bytes  328,945.78 bytes/sec
total size is 40,893,007  speedup is 27.63

 Fetching remote list...
 Fetch Ok

 Syncing selected overlay(s)...
 Running Rsync... # /usr/bin/rsync -rlptDvz --progress --delete --delete-after --timeout=180 --exclude=distfiles/* --exclude=local/* --exclude=packages/* rsync://roverlay.dev.gentoo.org/roverlay/ /var/lib/layman/roverlay
 Running Git... # ( cd /var/lib/layman/science  && /usr/bin/git pull )
 Failure result returned from Git
  
 Succeeded:
 ------
 Successfully synchronized overlay "roverlay".
  
  
 Errors:
 ------
 Failed to sync overlay "science".
 Error was: Syncing overlay "science" returned status 1!
 db.sync()
  

 CLI: Errors occurred processing action sync_all
  
 Errors:
 ------
 Failed to sync overlay "science".
 Syncing overlay "science" returned status 1!
 db.sync()
  

François Bissey | 17 Oct 03:43 2014
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git migration guide

Hi all,

Do we have a migration guide from git-2 to git-r3.
Google was lacking in providing info.

Francois

v_2e | 20 Sep 11:56 2014
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[sage-on-gentoo] Cannot install sage-doc: insufficient memory

  Hello!
  I have been experiencing a problem trying to install sage-doc for
several months. I have 2GB of RAM on my laptop, and it turns out not
sufficient to build Sage documentation. Each time it fails with a
message "Cannot allocate memory". I use Xfce, so the system itself does
not consume too much memory. Therefore I do not understand if this is a
sage-doc problem or not.

  Regards,
    Vladimir

----- 
 <v_2e <at> ukr.net>

ferreirafm | 18 Sep 17:33 2014
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hdf-java

Hi GentooSci, 
Can't emerge hdf-java. The file hdf-java-2.9-src.tar can't be found in the tree.

Build.log is as follows:

>>> Downloading 'ftp://ftp.las.ic.unicamp.br/pub/gentoo/distfiles/hdf-java-2.9-src.tar'
pathconf: Permission denied
--2014-09-18 12:25:56--  ftp://ftp.las.ic.unicamp.br/pub/gentoo/distfiles/hdf-java-2.9-src.tar
           => ‘/usr/portage/distfiles/hdf-java-2.9-src.tar’
Resolving ftp.las.ic.unicamp.br... 143.106.60.118
Connecting to ftp.las.ic.unicamp.br|143.106.60.118|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /pub/gentoo/distfiles ... done.
==> SIZE hdf-java-2.9-src.tar ... done.
==> PASV ... done.    ==> RETR hdf-java-2.9-src.tar ... 
No such file ‘hdf-java-2.9-src.tar’.

>>> Downloading 'http://www.las.ic.unicamp.br/pub/gentoo/distfiles/hdf-java-2.9-src.tar'
--2014-09-18 12:26:04--  http://www.las.ic.unicamp.br/pub/gentoo/distfiles/hdf-java-2.9-src.tar
Resolving www.las.ic.unicamp.br... 143.106.60.118
Connecting to www.las.ic.unicamp.br|143.106.60.118|:80... connected.
HTTP request sent, awaiting response... Read error (Connection timed out) in headers.
Retrying.

--2014-09-18 12:27:05--  (try: 2)  http://www.las.ic.unicamp.br/pub/gentoo/distfiles/hdf-java-2.9-src.tar
Connecting to www.las.ic.unicamp.br|143.106.60.118|:80... connected.
HTTP request sent, awaiting response... Read error (Connection timed out) in headers.
Retrying.

--2014-09-18 12:28:14--  (try: 3)  http://www.las.ic.unicamp.br/pub/gentoo/distfiles/hdf-java-2.9-src.tar
Connecting to www.las.ic.unicamp.br|143.106.60.118|:80... connected.
HTTP request sent, awaiting response... Read error (Connection timed out) in headers.
Giving up.

>>> Downloading 'ftp://ftp.ussg.iu.edu/pub/linux/gentoo/distfiles/hdf-java-2.9-src.tar'
pathconf: Permission denied
--2014-09-18 12:29:16--  ftp://ftp.ussg.iu.edu/pub/linux/gentoo/distfiles/hdf-java-2.9-src.tar
           => ‘/usr/portage/distfiles/hdf-java-2.9-src.tar’
Resolving ftp.ussg.iu.edu... 156.56.247.193
Connecting to ftp.ussg.iu.edu|156.56.247.193|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /pub/linux/gentoo/distfiles ... done.
==> SIZE hdf-java-2.9-src.tar ... done.
==> PASV ... done.    ==> RETR hdf-java-2.9-src.tar ... 
No such file ‘hdf-java-2.9-src.tar’.

>>> Downloading 'ftp://mirror.iawnet.sandia.gov/pub/gentoo/distfiles/hdf-java-2.9-src.tar'
pathconf: Permission denied
--2014-09-18 12:29:22--  ftp://mirror.iawnet.sandia.gov/pub/gentoo/distfiles/hdf-java-2.9-src.tar
           => ‘/usr/portage/distfiles/hdf-java-2.9-src.tar’
Resolving mirror.iawnet.sandia.gov... 192.160.227.246
Connecting to mirror.iawnet.sandia.gov|192.160.227.246|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /pub/gentoo/distfiles ... done.
==> SIZE hdf-java-2.9-src.tar ... done.
==> PASV ... done.    ==> RETR hdf-java-2.9-src.tar ... 
No such file ‘hdf-java-2.9-src.tar’.

>>> Downloading 'http://www.hdfgroup.org/ftp/HDF5/hdf-java/src/hdf-java-2.9-src.tar'
--2014-09-18 12:29:34--  http://www.hdfgroup.org/ftp/HDF5/hdf-java/src/hdf-java-2.9-src.tar
Resolving www.hdfgroup.org... 50.28.50.143
Connecting to www.hdfgroup.org|50.28.50.143|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2014-09-18 12:29:35 ERROR 404: Not Found.

[31;01m * [39;49;00mFetch failed for 'dev-java/hdf-java-2.9', Log file:
[31;01m * [39;49;00m '/var/tmp/portage/dev-java/hdf-java-2.9/temp/build.log'

Jauhien Piatlicki | 11 Sep 17:57 2014
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science eselect fork

Hi,

I'm just wondering what is the status of our eselect fork and what
blocks adding patches back to the upstream?

--
Jauhien

Jauhien Piatlicki | 2 Sep 18:42 2014
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packages with invalid SRC_URI and compilation failures

Hi,

I would ask an opinion about what to do with packages that have invalid
SRC_URI (pointing to non-existent sources) and severe compilation problems.

I'm trying to fix ebuilds that lead to `repoman full` failures now, so
we will be able to have automatic repoman checks for pull requests. Some
ebuilds are really outdated and quite hard to fix (e.g. I tried to do
version bump for sci-physics/bigdft, but I failed as new version does
not compile and error is in fortran code, that I do not understand).

So what to do with such outdated not working stuff? As nobody makes
issues/bugs about it, I think, we can just remove unmaintained broken
packages from the overlay.

--
Jauhien

Thomas Kahle | 18 Aug 13:43 2014
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Sage keyword files

Hi,

here are two additions to the provided keyword files (one keyword one
USE actually) that seem necessary for sage-6.3 on stable Gentoo:

The following keyword changes are necessary to proceed:
 (see "package.accept_keywords" in the portage(5) man page for more details)
# required by sci-mathematics/sage-6.3::sage-on-gentoo
# required by sci-mathematics/sage-doc-6.3::sage-on-gentoo
=dev-python/numpy-1.8.1 ~amd64

The following USE changes are necessary to proceed:
 (see "package.use" in the portage(5) man page for more details)
# required by sci-mathematics/sage-6.3::sage-on-gentoo
# required by sci-mathematics/sage-doc-6.3::sage-on-gentoo
>=sci-libs/libsingular-3.1.6-r3 flint

Thanks,
Thomas

marco restelli | 29 Jul 15:43 2014
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petsc-3.5.1, missing fortran includes

Hi all,
   I notice that  petsc-3.5.1.ebuild  does not install some include
files which are useful when using the fortran interface of PETSC; for
me the problem is solved adding

191a192,196
> 		doins include/finclude/*.h90
> 		insinto /usr/include/${PN}/finclude/ftn-auto
> 		doins include/finclude/ftn-auto/*
> 		insinto /usr/include/${PN}/finclude/ftn-custom
> 		doins include/finclude/ftn-custom/*

Regards,
   Marco

v_2e | 17 Jul 17:47 2014
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[sage-on-gentoo] too big 'doctrees' folder

  Hello!
  Today I noticed this catalog on my system:

  /usr/share/doc/sage/output/doctrees

  It takes about 850 MB of disk space. There are also separate folders 
  /usr/share/doc/sage/(en,pt,tr,ru,de,fr)
  /usr/share/doc/sage/output/html/*
containing the RST sources and HTML files of Sage reference and all
related stuff.

  So my question is: what is this 'doctrees' folder is actually for? Do
we really need it? Is it safe to remove it?

  And by the way, is it (will it be) possible to install only a
selected set of languages for the Sage help files?

  Regards,
    Vladimir

----- 
 <v_2e <at> ukr.net>

eduardo lenz | 17 Jul 17:47 2014
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Resposta automática

This account is not active. Please send e-mails to lenz <at> joinville.udesc.br.

François Bissey | 2 Jul 12:40 2014
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overlay and github out of sync again

Hi,

The overlay are out of sync again. When jlec merged pynomo
earlier today it wasn’t pushed to the Gentoo overlay for a reason
or another.
And then I pushed a minor keywording for x64-macos and it did
go on the Gentoo overlay but not on github.

I cannot remember how to resolve the problem, do we have documentation
elsewhere than on the mailing list in post several years old for that?

François


Gmane