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

Justin (jlec | 2 Jul 08:46 2014
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Help wanted

Dear users,

as you all know the science team is short of manpower. And therefore bug
fixing can have a long delay.

We need your help with fixing bugs!

The procedure is simple,

* Figure out how to fix the bug
* Move the package to the science overlay on github [1] and add the fix
* Send a pull-request and tell us to move the fix into the tree
* Add a notice to bugzilla that there is a fix in the overlay
* Keep pushing us if we do not reimport your fix to the tree

And of course, if you get fun in doing package maintaining we are always
happy to recruit new developers.

Thanks for your help,
Justin

1)
https://github.com/gentoo-science/sci/blob/master/CONTRIBUTING.md

Thomas Kahle | 26 Jun 13:33 2014
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flint to the main tree?

Hi,

what do you think about moving flint to the main tree?  It recently
became a dependency of my beloved Macaulay2 (currently only in the git
version) but at some point I'll need for the main tree version of M2.

Any objections?

Cheers,
Thomas

Bastian Löffler | 9 Jun 13:25 2014
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Trouble building scipy-0.14.0 against acml











Hi all, I can not build scipy 0.14.0 agaonst the currenct aclm since it complains a missing blas: numpy.distutils.system_info.BlasNotFoundError: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. * ERROR: sci-libs/scipy-0.14.0::gentoo failed (compile phase): * (no error message) * * Call stack: * ebuild.sh, line 93: Called src_compile * environment, line 4075: Called distutils-r1_src_compile * environment, line 1421: Called _distutils-r1_run_foreach_impl 'python_compile' * environment, line 312: Called python_parallel_foreach_impl 'distutils-r1_run_phase' 'python_compile' * environment, line 3808: Called multibuild_parallel_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile' * environment, line 2855: Called multibuild_foreach_variant '_multibuild_parallel' '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile' * environment, line 2798: Called _multibuild_run '_multibuild_parallel' '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile' * environment, line 2796: Called _multibuild_parallel '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile' * environment, line 2846: Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'python_compile' * environment, line 914: Called distutils-r1_run_phase 'python_compile' * environment, line 1412: Called python_compile * environment, line 3315: Called distutils-r1_python_compile 'config_fc' '--noopt' '--noarch' * environment, line 1292: Called esetup.py 'build' 'config_fc' '--noopt' '--noarch' * environment, line 1862: Called die * The specific snippet of code: * "${ <at> }" || die * * If you need support, post the output of `emerge --info '=sci-libs/scipy-0.14.0::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-libs/scipy-0.14.0::gentoo'`. * The complete build log is located at '/var/tmp/portage/sci-libs/scipy-0.14.0/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-libs/scipy-0.14.0/temp/environment'. * Working directory: '/var/tmp/portage/sci-libs/scipy-0.14.0/work/scipy-0.14.0-python2_7' * S: '/var/tmp/portage/sci-libs/scipy-0.14.0/work/scipy-0.14.0' /usr/lib64/portage/bin/isolated-functions.sh: line 226: kill: (6675) - No such process blas_opt_info: system_info: NOT AVAILABLE blas_info: libraries not found in ['/usr/lib64'] NOT AVAILABLE blas_src_info: NOT AVAILABLE /usr/lib64/python3.3/distutils/dist.py:258: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib64/python3.3/site-packages/numpy/distutils/system_info.py:1511: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) /usr/lib64/python3.3/site-packages/numpy/distutils/system_info.py:566: UserWarning: Specified path is invalid. warnings.warn('Specified path %s is invalid.' % d) /usr/lib64/python3.3/site-packages/numpy/distutils/system_info.py:1520: UserWarning: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. warnings.warn(BlasNotFoundError.__doc__) /usr/lib64/python3.3/site-packages/numpy/distutils/system_info.py:1523: UserWarning: Blas (http://www.netlib.org/blas/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [blas_src]) or by setting the BLAS_SRC environment variable. warnings.warn(BlasSrcNotFoundError.__doc__) Traceback (most recent call last): File "setup.py", line 237, in <module> setup_package() File "setup.py", line 234, in setup_package setup(**metadata) File "/usr/lib64/python3.3/site-packages/numpy/distutils/core.py", line 135, in setup config = configuration() File "setup.py", line 173, in configuration config.add_subpackage('scipy') File "/usr/lib64/python3.3/site-packages/numpy/distutils/misc_util.py", line 966, in add_subpackage caller_level = 2) File "/usr/lib64/python3.3/site-packages/numpy/distutils/misc_util.py", line 935, in get_subpackage caller_level = caller_level + 1) File "/usr/lib64/python3.3/site-packages/numpy/distutils/misc_util.py", line 872, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "scipy/setup.py", line 12, in configuration config.add_subpackage('integrate') File "/usr/lib64/python3.3/site-packages/numpy/distutils/misc_util.py", line 966, in add_subpackage caller_level = 2) File "/usr/lib64/python3.3/site-packages/numpy/distutils/misc_util.py", line 935, in get_subpackage caller_level = caller_level + 1) File "/usr/lib64/python3.3/site-packages/numpy/distutils/misc_util.py", line 872, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "scipy/integrate/setup.py", line 12, in configuration blas_opt = get_info('blas_opt',notfound_action=2) File "/usr/lib64/python3.3/site-packages/numpy/distutils/system_info.py", line 340, in get_info return cl().get_info(notfound_action) File "/usr/lib64/python3.3/site-packages/numpy/distutils/system_info.py", line 499, in get_info raise self.notfounderror(self.notfounderror.__doc__) numpy.distutils.system_info.BlasNotFoundError: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. * ERROR: sci-libs/scipy-0.14.0::gentoo failed (compile phase): * (no error message) * * Call stack: * ebuild.sh, line 93: Called src_compile * environment, line 4075: Called distutils-r1_src_compile * environment, line 1421: Called _distutils-r1_run_foreach_impl 'python_compile' * environment, line 312: Called python_parallel_foreach_impl 'distutils-r1_run_phase' 'python_compile' * environment, line 3808: Called multibuild_parallel_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile' * environment, line 2855: Called multibuild_foreach_variant '_multibuild_parallel' '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile' * environment, line 2798: Called _multibuild_run '_multibuild_parallel' '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile' * environment, line 2796: Called _multibuild_parallel '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile' * environment, line 2846: Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'python_compile' * environment, line 914: Called distutils-r1_run_phase 'python_compile' * environment, line 1412: Called python_compile * environment, line 3315: Called distutils-r1_python_compile 'config_fc' '--noopt' '--noarch' * environment, line 1292: Called esetup.py 'build' 'config_fc' '--noopt' '--noarch' * environment, line 1862: Called die * The specific snippet of code: * "${ <at> }" || die * * If you need support, post the output of `emerge --info '=sci-libs/scipy-0.14.0::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-libs/scipy-0.14.0::gentoo'`. * The complete build log is located at '/var/tmp/portage/sci-libs/scipy-0.14.0/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-libs/scipy-0.14.0/temp/environment'. * Working directory: '/var/tmp/portage/sci-libs/scipy-0.14.0/work/scipy-0.14.0-python3_3' * S: '/var/tmp/portage/sci-libs/scipy-0.14.0/work/scipy-0.14.0' /usr/lib64/portage/bin/isolated-functions.sh: line 226: kill: (6675) - No such process >>> Failed to emerge sci-libs/scipy-0.14.0, Log file:


Gmane