[gentoo-science] packages with invalid SRC_URI and compilation failures

[gentoo-science] packages with invalid SRC_URI and compilation failures

[Jauhien Piatlicki]

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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ebuilds are really outdated and quite hard to fix (e.g. I tried to do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So what to do with such outdated not working stuff?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


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Re: [gentoo-science] packages with invalid SRC_URI and compilation failures

[François Bissey]

On Tue, 02 Sep 2014 18:42:19 Jauhien Piatlicki wrote:
> 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 ebuilds are really outdated and quite hard to fix (e.g. I tried to do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 So what to do with such outdated not working stuff?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.
>

I guess if someone is using it they will complain. Then it can be their
job to fix it :)

Francois

Re: [gentoo-science] packages with invalid SRC_URI and compilation failures

[Jauhien Piatlicki]

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Hi,

03.09.14 02:10, François Bissey написав(ла):
> I guess if someone is using it they will complain. Then it can be their
> job to fix it :)

the problem is that such packages can not be compiled => can not be used. So I see no reason to complain, as availability of such ebuilds in the tree does not help to install appropriate software. And if once a person that used it, will want to fix it, he or she can just pick the ebuild from the git history.

--
Jauhien




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Re: [gentoo-science] packages with invalid SRC_URI and compilation failures

[Honza Macháček]

On 09/03/2014 02:10 AM, François Bissey wrote:
> On Tue, 02 Sep 2014 18:42:19 Jauhien Piatlicki wrote:
> >...(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).
>
> I guess if someone is using it they will complain. Then it can be their
> job to fix it :)

Fixing sci-physics/bigdft should be my job. I'm only rather slow with that. Send
any complaints, info or advice to me; I may not respond, and even no
improvements to the ebuild may come up for quite a long time afterwards, but I
will be working on it.

All the best.

Honza Macháček

Re: [gentoo-science] packages with invalid SRC_URI and compilation failures

[Jauhien Piatlicki]

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03.09.14 09:53, Honza Macháček написав(ла):
> On 09/03/2014 02:10 AM, François Bissey wrote:
>> On Tue, 02 Sep 2014 18:42:19 Jauhien Piatlicki wrote:
>>> ...(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).
>>
>> I guess if someone is using it they will complain. Then it can be their
>> job to fix it :)
> 
> Fixing sci-physics/bigdft should be my job. I'm only rather slow with that. Send
> any complaints, info or advice to me; I may not respond, and even no
> improvements to the ebuild may come up for quite a long time afterwards, but I
> will be working on it.


sci-physics/bigdft is not the worst case. ) It only needs only version bump and little ebuild clean up. After of it you'll need to fix compilation failure because compiler complains about using f_malloc and f_free from flib with one of variables.

--
Jauhien



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Re: [gentoo-science] packages with invalid SRC_URI and compilation failures

[François Bissey]

Do you have a list, for people interested?

François
On 3/09/2014, at 20:01, Jauhien Piatlicki <jauhien@gentoo.org> wrote:

> 03.09.14 09:53, Honza Macháček написав(ла):
>> On 09/03/2014 02:10 AM, François Bissey wrote:
>>> On Tue, 02 Sep 2014 18:42:19 Jauhien Piatlicki wrote:
>>>> ...(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).
>>> 
>>> I guess if someone is using it they will complain. Then it can be their
>>> job to fix it :)
>> 
>> Fixing sci-physics/bigdft should be my job. I'm only rather slow with that. Send
>> any complaints, info or advice to me; I may not respond, and even no
>> improvements to the ebuild may come up for quite a long time afterwards, but I
>> will be working on it.
> 
> 
> sci-physics/bigdft is not the worst case. ) It only needs only version bump and little ebuild clean up. After of it you'll need to fix compilation failure because compiler complains about using f_malloc and f_free from flib with one of variables.
> 
> --
> Jauhien
> 
> 

Re: [gentoo-science] packages with invalid SRC_URI and compilation failures

[Jauhien Piatlicki]

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Hi,

On 09/03/2014 11:22 AM, François Bissey wrote:
> Do you have a list, for people interested?
> 

generating it now. I'll send it to the list later.

--
Jauhien


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Re: [gentoo-science] packages with invalid SRC_URI and compilation failures

[Jauhien Piatlicki]

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Hi,

On 09/03/2014 11:22 AM, François Bissey wrote:> Do you have a list, for
people interested?
>

list of packages with SRC_URI failure problems is attached.

List of packages with repoman problem can be obtained by running
`repoman full -d` (c) Captain Obvious

I can not create list of packages with really hard problems as this
needs more work, that is in progress now.

What I'm planning to do is:

- try to fix repoman failures

- try to do version bump for packages with repoman failures/SRC_URI failures

- if this does not help, mask the package, or remove bad versions, if a
package has other, working, versions

I think this will not hurt people interested in a given package. I will
describe in mask comment what exact problems I had, so it would be
easier for those interested to fix it. I think it is the sanest way to

- silence repoman, so new PR can be tested automatically

- make sure that stuff from our overlay is working

- signal to ones interested in a given package, that there is something
bad with it and it should be fixed

Regards,
Jauhien

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* Messages for package app-admin/eselect-1.3.7-r100:

 * The following are listed in SRC_URI for eselect:
 *    mirror://gentoo/eselect-1.3.7.tar.xz

 * Messages for package app-doc/blacs-docs-1.1:

 * The following are listed in SRC_URI for blacs-docs:
 *    mirror://gentoo/blacs-docs-1.1.tar.bz2

 * Messages for package app-vim/freefem++-syntax-20081108-r1:

 * The following are listed in SRC_URI for freefem++-syntax:
 *    http://omploader.org/vMWlraw/freefem++-syntax-20081108.tar.gz

 * Messages for package dev-java/gluegen-1_p20080421:

 * The following are listed in SRC_URI for gluegen:
 *    http://dev.gentoo.org/~ali_bush/distfiles/gluegen-20080421.tar.bz2

 * Messages for package dev-java/hdf-java-2.9:

 * The following are listed in SRC_URI for hdf-java:
 *    http://www.hdfgroup.org/ftp/HDF5/hdf-java/src/hdf-java-2.9-src.tar

 * Messages for package dev-java/jhealpix-3.11:

 * The following are listed in SRC_URI for jhealpix:
 *    mirror://sourceforge/jhealpix/Healpix_3.11/Healpix_3.11_2013Apr24.tar.gz

 * Messages for package dev-java/vecmath-1.5.1:

 * The following are listed in SRC_URI for vecmath:
 *    http://dev.gentoo.org/~ali_bush/distfiles/vecmath-1.5.1.tar.bz2
 *    test?
 *    (
 *    http://dev.gentoo.org/~ali_bush/distfiles/vecmath-test-1.5.1.tar.bz2
 *    )

 * Messages for package dev-libs/asmjit-1.0_beta4:

 * The following are listed in SRC_URI for asmjit:
 *    http://asmjit.googlecode.com/files/AsmJit-1.0-beta4.zip

 * Messages for package dev-libs/simclist-1.6:

 * The following are listed in SRC_URI for simclist:
 *    http://mij.oltrelinux.com/devel/simclist/simclist-1.6.tar.bz2

 * Messages for package dev-ml/gsl-ocaml-1.10.2:

 * The following are listed in SRC_URI for gsl-ocaml:
 *    http://bitbucket.org/mmottl/gsl-ocaml/downloads/gsl-ocaml-1.10.2.tar.gz

 * Messages for package dev-ml/lacaml-7.0.3:

 * The following are listed in SRC_URI for lacaml:
 *    https://bitbucket.org/mmottl/lacaml/downloads/lacaml-7.0.3.tar.gz

 * Messages for package dev-python/inference-0.4:

 * The following are listed in SRC_URI for inference:
 *    http://inference.astro.cornell.edu//inference-0.4.tar.gz

 * Messages for package dev-python/psubprocess-0.1.2:

 * The following are listed in SRC_URI for psubprocess:
 *    http://bioinf.comav.upv.es/_downloads/psubprocess-0.1.2.tar.gz

 * Messages for package dev-python/ufl-0.5.4:

 * The following are listed in SRC_URI for ufl:
 *    http://launchpad.net/ufl/trunk/0.5.4/+download/ufl-0.5.4.tar.gz

 * Messages for package dev-util/VampirTrace-5.14.3:

 * The following are listed in SRC_URI for VampirTrace:
 *    http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=vampirtrace&get=VampirTrace-5.14.3.tar.gz

 * Messages for package dev-util/f90cache-0.94:

 * The following are listed in SRC_URI for f90cache:
 *    http://people.irisa.fr/Edouard.Canot/f90cache/f90cache-0.94.tar.bz2

 * Messages for package net-firewall/gcb-1.5.6:

 * The following are listed in SRC_URI for gcb:
 *    http://www.cs.wisc.edu/condor/gcb/download/gcb-1.5.6.tar.gz

 * Messages for package sci-astronomy/bpz-1.99.3:

 * The following are listed in SRC_URI for bpz:
 *    http://www.its.caltech.edu/~coe/BPZ//bpz-1.99.3.tar.gz

 * Messages for package sci-astronomy/casapy-bin-4.2.0.28322.021_p1:

 * The following are listed in SRC_URI for casapy-bin:
 *    https://svn.cv.nrao.edu/casa/linux_distro/casapy-42.0.28322-021-1-64b.tar.gz

 * Messages for package sci-astronomy/healpix_idl-3.11:

 * The following are listed in SRC_URI for healpix_idl:
 *    mirror://sourceforge/healpix_idl/Healpix_3.11/Healpix_3.11_2013Apr24.tar.gz

 * Messages for package sci-biology/Atlas-Link-0.01:

 * The following are listed in SRC_URI for Atlas-Link:
 *    https://www.hgsc.bcm.edu/sites/default/files/software/Atlas_Link/Atlas-link.tar.gz

 * Messages for package sci-biology/MagicViewer-1.2.1:

 * The following are listed in SRC_URI for MagicViewer:
 *    http://59.79.168.90/soft/MagicViewer_1.2.1_x86_64_linux.tar.gz
 *    http://59.79.168.90/soft/MagicViewer_1.2.1_x86_32_linux.tar.gz

 * Messages for package sci-biology/OBO-Edit-2.1.0:

 * The following are listed in SRC_URI for OBO-Edit:
 *    http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%202.1.0/2-1-0_unix_install4j.sh/download
 *    ->
 *    OBO-Edit_unix_install4j-2.1.0.sh
 *    http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%202.1.0/ReleaseNotes-2.1.0.txt

 * Messages for package sci-biology/ONTO-PERL-1.31:

 * The following are listed in SRC_URI for ONTO-PERL:
 *    mirror://cpan/authors/id/E/EA/EASR/ONTO-PERL/ONTO-PERL-1.31.tar.gz

 * Messages for package sci-biology/amos-short-0.9.3:

 * The following are listed in SRC_URI for amos-short:
 *    http://sourceforge.net/projects/amos/files/short_read_assembly/0.9.3/AMOS-short.tgz

 * Messages for package sci-biology/cgview-bin-20131130:

 * The following are listed in SRC_URI for cgview-bin:
 *    http://www.ualberta.ca/~stothard/downloads/cgview_comparison_tool.zip

 * Messages for package sci-biology/embassy-cbstools-1.0.0-r3:

 * The following are listed in SRC_URI for embassy-cbstools:
 *    ftp://emboss.open-bio.org/pub/EMBOSS/CBSTOOLS-1.0.0.tar.gz
 *    ->
 *    embassy-cbstools-1.0.0-r3.tar.gz

 * Messages for package sci-biology/embassy-domainatrix-0.1.0-r6:

 * The following are listed in SRC_URI for embassy-domainatrix:
 *    ftp://emboss.open-bio.org/pub/EMBOSS/DOMAINATRIX-0.1.0.tar.gz
 *    ->
 *    embassy-domainatrix-0.1.0-r6.tar.gz

 * Messages for package sci-biology/embassy-domalign-0.1.0-r5:

 * The following are listed in SRC_URI for embassy-domalign:
 *    ftp://emboss.open-bio.org/pub/EMBOSS/DOMALIGN-0.1.0.tar.gz
 *    ->
 *    embassy-domalign-0.1.0-r5.tar.gz

 * Messages for package sci-biology/embassy-domsearch-0.1.0-r5:

 * The following are listed in SRC_URI for embassy-domsearch:
 *    ftp://emboss.open-bio.org/pub/EMBOSS/DOMSEARCH-0.1.0.tar.gz
 *    ->
 *    embassy-domsearch-0.1.0-r5.tar.gz

 * Messages for package sci-biology/embassy-emnu-1.05-r7:

 * The following are listed in SRC_URI for embassy-emnu:
 *    ftp://emboss.open-bio.org/pub/EMBOSS/EMNU-1.05.tar.gz
 *    ->
 *    embassy-emnu-1.05-r7.tar.gz

 * Messages for package sci-biology/embassy-esim4-1.0.0-r7:

 * The following are listed in SRC_URI for embassy-esim4:
 *    ftp://emboss.open-bio.org/pub/EMBOSS/ESIM4-1.0.0.tar.gz
 *    ->
 *    embassy-esim4-1.0.0-r7.tar.gz

 * Messages for package sci-biology/embassy-hmmer-2.3.2-r4:

 * The following are listed in SRC_URI for embassy-hmmer:
 *    ftp://emboss.open-bio.org/pub/EMBOSS/HMMER-2.3.2.tar.gz
 *    ->
 *    embassy-hmmer-2.3.2-r4.tar.gz

 * Messages for package sci-biology/embassy-iprscan-4.3.1-r2:

 * The following are listed in SRC_URI for embassy-iprscan:
 *    ftp://emboss.open-bio.org/pub/EMBOSS/IPRSCAN-4.3.1.tar.gz
 *    ->
 *    embassy-iprscan-4.3.1-r2.tar.gz

 * Messages for package sci-biology/embassy-mse-3.0.0:

 * The following are listed in SRC_URI for embassy-mse:
 *    ftp://emboss.open-bio.org/pub/EMBOSS/MSE-3.0.0.tar.gz
 *    ->
 *    embassy-mse-3.0.0.tar.gz

 * Messages for package sci-biology/embassy-phylipnew-3.69:

 * The following are listed in SRC_URI for embassy-phylipnew:
 *    ftp://emboss.open-bio.org/pub/EMBOSS/PHYLIPNEW-3.69.tar.gz
 *    ->
 *    embassy-phylipnew-3.69.tar.gz

 * Messages for package sci-biology/embassy-signature-0.1.0-r5:

 * The following are listed in SRC_URI for embassy-signature:
 *    ftp://emboss.open-bio.org/pub/EMBOSS/SIGNATURE-0.1.0.tar.gz
 *    ->
 *    embassy-signature-0.1.0-r5.tar.gz

 * Messages for package sci-biology/embassy-structure-0.1.0-r5:

 * The following are listed in SRC_URI for embassy-structure:
 *    ftp://emboss.open-bio.org/pub/EMBOSS/STRUCTURE-0.1.0.tar.gz
 *    ->
 *    embassy-structure-0.1.0-r5.tar.gz

 * Messages for package sci-biology/embassy-topo-2.0.0:

 * The following are listed in SRC_URI for embassy-topo:
 *    ftp://emboss.open-bio.org/pub/EMBOSS/TOPO-2.0.0.tar.gz
 *    ->
 *    embassy-topo-2.0.0.tar.gz

 * Messages for package sci-biology/embassy-vienna-1.7.2-r2:

 * The following are listed in SRC_URI for embassy-vienna:
 *    ftp://emboss.open-bio.org/pub/EMBOSS/VIENNA-1.7.2.tar.gz
 *    ->
 *    embassy-vienna-1.7.2-r2.tar.gz

 * Messages for package sci-biology/emboss-6.3.1_p4-r2:

 * The following are listed in SRC_URI for emboss:
 *    ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.3.1.tar.gz
 *    http://dev.gentoo.org/~jlec/distfiles/emboss-6.3.1_p4-r2.patch.bz2
 *    http://pkgs.fedoraproject.org/lookaside/pkgs/EMBOSS/patch-1-4.gz/7a42594c5eda4adc6457f33e4ab0d8f2/patch-1-4.gz
 *    ->
 *    emboss-6.3.1_p4-upstream.patch.gz

 * Messages for package sci-biology/est2uni-0.27:

 * The following are listed in SRC_URI for est2uni:
 *    http://cichlid.umd.edu/est2uni/est2uni_0.27.tar.gz
 *    ftp://ftp.ncbi.nih.gov/pub/UniVec/UniVec
 *    ftp://ftp.ncbi.nih.gov/pub/UniVec/UniVec_Core
 *    http://www.geneontology.org/ontology/gene_ontology.obo
 *    http://www.geneontology.org/doc/GO.terms_and_ids

 * Messages for package sci-biology/fastdnaml-1.2.2:

 * The following are listed in SRC_URI for fastdnaml:
 *    mirror://debian/pool/main/f/fastdnaml/fastdnaml_1.2.2.orig.tar.gz
 *    mirror://debian/pool/main/f/fastdnaml/fastdnaml_1.2.2-8.diff.gz

 * Messages for package sci-biology/mapview-bin-3.4.1:

 * The following are listed in SRC_URI for mapview-bin:
 *    http://evolution.sysu.edu.cn/software/mapview.rar
 *    http://evolution.sysu.edu.cn/mapview/MVF.pdf

 * Messages for package sci-biology/mira-4.0_rc4:

 * The following are listed in SRC_URI for mira:
 *    http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/mira-4.0rc4.tar.bz2
 *    mirror://sourceforge/mira-assembler/mira_3rdparty_06-07-2012.tar.bz2

 * Messages for package sci-biology/ngs_backbone-1.4.0:

 * The following are listed in SRC_URI for ngs_backbone:
 *    http://bioinf.comav.upv.es/_downloads/ngs_backbone-1.4.0.tar.gz

 * Messages for package sci-biology/rnaplex-0.2:

 * The following are listed in SRC_URI for rnaplex:
 *    http://www.tbi.univie.ac.at/~htafer/RNAplex/RNAplex-0.2.tar.gz

 * Messages for package sci-biology/sra_sdk-2.1.6:

 * The following are listed in SRC_URI for sra_sdk:
 *    http://trace.ncbi.nlm.nih.gov/Traces/sra/static/sra_sdk-2.1.6.tar.gz

 * Messages for package sci-biology/swissknife-1.67:

 * The following are listed in SRC_URI for swissknife:
 *    ftp://ftp.ebi.ac.uk/pub/software/swissprot/Swissknife/Swissknife_1.67.tar.gz

 * Messages for package sci-biology/symap-4.0:

 * Please register and download symap_4.0.tar.gz (110MB)
 * at http://www.agcol.arizona.edu/software/symap/v4.0/download/
 * and place it in /usr/portage/distfiles

 * Messages for package sci-biology/tablet-bin-1.13.12.17:

 * The following are listed in SRC_URI for tablet-bin:
 *    x86?
 *    (
 *    http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x86_1_13_12_17.sh
 *    ->
 *    tablet-bin-1.13.12.17.sh
 *    )
 *    amd64?
 *    (
 *    http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x64_1_13_12_17.sh
 *    ->
 *    tablet-bin-1.13.12.17.sh
 *    )
 *    http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py

 * Messages for package sci-biology/tigr-assembler-2.0:

 * The following are listed in SRC_URI for tigr-assembler:
 *    ftp://ftp.tigr.org/pub/software/assembler/TIGR_Assembler_v2.tar.gz

 * Messages for package sci-chemistry/bist-0.5.1-r1:

 * The following are listed in SRC_URI for bist:
 *    http://www.autistici.org/interzona/ftrack.php?url=sections/06_Download/bist-0.5.1.tar.gz

 * Messages for package sci-chemistry/chimera-bin-1.6.2:

 * Please visit
 * http://www.cgl.ucsf.edu/chimera/download.html
 * and download chimera-1.6.2-linux_x86_64.bin into /usr/portage/distfiles

 * Messages for package sci-chemistry/cpmgfit-1.43:

 * The following are listed in SRC_URI for cpmgfit:
 *    http://biochemistry.hs.columbia.edu/labs/palmer/software/cpmgfit.linux.tar.gz
 *    ->
 *    cpmgfit-1.43.tar.gz

 * Messages for package sci-chemistry/gamess-20130501.1:

 * Please download gamess-current.tar.gz from
 * http://www.msg.ameslab.gov/GAMESS/License_Agreement.html.
 * Be sure to select the version 1 MAY 2013 (R1) tarball!!
 * Then move the tarball to
 * /usr/portage/distfiles/gamess-20130501.1.tar.gz

 * Messages for package sci-chemistry/jana2000-20071218:

 * The following are listed in SRC_URI for jana2000:
 *    ftp://ftp.fzu.cz/pub/cryst/beta2000/jana2000.tar.gz

 * Messages for package sci-chemistry/jligand-1.0.19:

 * The following are listed in SRC_URI for jligand:
 *    http://www.ysbl.york.ac.uk/mxstat/JLigand/JLigand.1.0.19.tar.gz

 * Messages for package sci-chemistry/module2-0_pre20140717:

 * Please download MODULE2.tar.gz from
 * http://www.ibs.fr/science-213/scientific-output/software/module/?lang=en
 * and place it in /usr/portage/distfiles

 * Messages for package sci-chemistry/mtz2hkl-0.3:

 * The following are listed in SRC_URI for mtz2hkl:
 *    http://shelx.uni-ac.gwdg.de/~tg/mtz2x/mtz2hkl/downloads/0.3/mtz2hkl_v0.3.tar.gz

 * Messages for package sci-chemistry/mtz2sca-0.3:

 * The following are listed in SRC_URI for mtz2sca:
 *    http://shelx.uni-ac.gwdg.de/~tg/mtz2x/mtz2sca/binaries/0.3/mtz2sca_v0.3.tar.gz

 * Messages for package sci-chemistry/panav-0.20130730:

 * The following are listed in SRC_URI for panav:
 *    http://www.wishartlab.com/download/PANAV.zip
 *    ->
 *    panav-0.20130730.zip

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