docking-related
articles).
I've created account on alioth (username - latticetower-guest), I also like
git.
Tanya.
-- Forwarded message --
From: Andreas Tille
Date: 2016-03-17 10:51 GMT+03:00
Subject: Re: Outreachy project (CI for all biological applications inside
Debian)
To: me
Hi Andreas,
I've decided to start with Concavity.
Is there a sample of a well-test-covered package?
Tanya
2016-03-21 10:27 GMT+03:00 Andreas Tille :
> Hi Tanya,
>
> On Mon, Mar 21, 2016 at 08:26:17AM +0300, merlettaia wrote:
> > My name is Tatiana Malygina, I'm anot
Hi Canberk!
And I'm an Outreachy intern.
While applying, I picked some packages I want to start with:
https://gist.github.com/latticetower/4402a17488c1629a78595bf4c9ec9b50
But I haven't discussed that plan with you yet. Please tell if you like to
do tests for some of these packages.
Do you have
Hi, Canberk and Andreas!
20.05.2016 11:29 пользователь "Andreas Tille" написал:
>
> Hi Canberk,
>
> On Fri, May 20, 2016 at 04:04:08AM +0300, Canberk Koç wrote:
> > Hello Andreas,
> >
> > I execute script succesfully and have a list at last thank you :-) I
look
> > them and consider i start with
Hi Michael!
> It might also help if you would add her to the DebiChem team
> > to enable her direct commit permissions.
>
> What's her alioth username?
>
My username is latticetower-guest
>
>
> Michael
>
--
Regards,
Tanya.
Hi, Canberk and all!
2016-05-24 2:57 GMT+03:00 Canberk Koç :
> Hello everyone,
>
> I use adt-run to my autopkgtest on exonerate and examine the outputs.
> I saw some failures but test run and give pass results.
> I decide to look their test files and saw they look for missing files
> error not o
Hi, Andreas (and Canberk, and All)!
I saw tests on exonerate and came up with idea what should be tested.
Is is ok if today I'll add several tests to concavity (the package I
started to add tests for at starting period), to check results of work with
other parameters and simple check of correctnes
Hi Andreas!
Sorry for not showing activity, I've experienced some strange technical
troubles with my VM :( It turned out that switching to unstable in
sources.list is not enough to work well with cme and testing packages from
unstable, now I fixed it (switched to virtual box with unstable Debian o
reliably available online
> today
> and tomorrow]
>
> Good morning Tanya,
>
> On Thu, Jun 02, 2016 at 08:37:36AM +0300, merlettaia wrote:
> > The test I wrote is unfinished - I had an error message when I tried to
> run
> > this simple test locally, now I'm stuck, a
Hi Andreas,
I finally found out what was wrong :)
2016-06-02 10:13 GMT+03:00 Andreas Tille :
>
> > Problem 2. When I run svn-buildpackage with current debian/install file,
> > these messages appear:
> > "...
> > /data/src/build-area/conservation-code-20110309.0/debian/install: 1:
> > /data/src/b
Hi Andreas,
2016-06-07 22:34 GMT+03:00 Andreas Tille :
>
>
> BTW, it makes sense to add the data files in debian/copyright where
> they are obtained from and under what license these can be used.
>
>
http://www.rcsb.org/pdb/static.do?p=general_information/about_pdb/policies_references.html
As des
Hi Andreas,
Yay! That's great!
And thank you for providing more verbose and clear text in README.test!
2016-06-08 15:26 GMT+03:00 Andreas Tille :
> Hi Tanya,
>
> On Wed, Jun 08, 2016 at 12:47:51PM +0300, merlettaia wrote:
> > Hi, Andreas!
> > I've checked concav
Hi Canberk,
The main difference between git and svn - svn always has only 1 (probably
remote) origin, and when you use svn commit (command looks similar to git
commit), your changes are sent directly to svn repository (in your case to
Alioth).
2016-06-13 10:26 GMT+03:00 Canberk Koç :
> Hi Afif,
>
Good morning, Andreas (and also all who reads this letter)!
First part of this letter is just to inform you, but I also have several
questions about packaging with perl for RostLab packages (questions are
given at the end of this letter).
0) First of all, this is what I did for now:
* Concavity,
ecided to postpone it and to fix later. Now I'll
try to install apbs from sources and check where the problem is - if you
don't mind.
2016-06-29 15:54 GMT+03:00 Andreas Tille :
> Hi Tanya,
>
> On Wed, Jun 29, 2016 at 01:35:38PM +0300, merlettaia wrote:
>
Hi Andreas,
2016-07-01 16:34 GMT+03:00 Andreas Tille :
> Hi Tanya,
>
> On Fri, Jul 01, 2016 at 12:09:36PM +0300, merlettaia wrote:
> > ...
> > least I tried to reproduce, it doesn't appear any more. Please check my
> > recent commit, and tell me if the error stil
Hi Andreas,
2016-07-02 0:32 GMT+03:00 Andreas Tille :
> Hi Tanya,
>
> On Fri, Jul 01, 2016 at 12:09:36PM +0300, merlettaia wrote:
> > That's why I think there
> > should be different order of commands, and this should fix that problem.
> At
> > least I tr
rofnet and try to
fix reprof.
2016-07-02 8:44 GMT+03:00 Andreas Tille :
> Hi Tanya,
>
> On Sat, Jul 02, 2016 at 01:50:20AM +0300, merlettaia wrote:
> >
> > It's optional in debian/control file, and it should be - pdb2pqr works
> > without it, and it simply shows
Hi Andreas,
When I run
debuild -us -uc -b
- for the first time, all goes fine.
When I run the same command again, I've got error message. Full error log
is in attached file.
2016-07-05 18:10 GMT+03:00 Andreas Tille :
> Hi Tanya,
>
> On Tue, Jul 05, 2016 at 04:39:18PM +0300, me
7;t find
any which doesn't produce segfault). How do you think?
2016-07-05 20:49 GMT+03:00 Andreas Tille :
> Hi Tanya,
>
> On Tue, Jul 05, 2016 at 07:30:28PM +0300, merlettaia wrote:
> > debuild -us -uc -b
>
> Hint: I'm using debuild which is a more intelligent w
Hi Andreas,
It would be fine to drop this line then.
I found a problem in which this package is involved also.
Last weekend I started to work on predictprotein. The hardest problem was
to make it work.
https://wiki.debian.org/DebianMed/PredictProtein - at some point I found
this instruction, spent
's why this test fails now and this reprof
update is not ready for upload.
2016-07-13 22:21 GMT+03:00 Andreas Tille :
> Hi Tanya,
>
> On Wed, Jul 13, 2016 at 07:24:12PM +0300, merlettaia wrote:
> >
> > I found a problem in which this package is involved also.
> > La
Hi Andreas,
For now I think I should better move forward.
I'll probably return to that package if I'll work on profphd (I tried to
update profphd to use current perl version, added testsuite, and then
decided to postpone it - and for now to fix all possible errors appearing
in predictprotein run -
Hi Andreas,
2016-07-14 10:51 GMT+03:00 Andreas Tille :
> [CC, ing other uploaders of reprof from rostlab]
> Hi Tanya,
>
> On Thu, Jul 14, 2016 at 10:32:44AM +0300, merlettaia wrote:
> > Hi Andreas,
> > I've added tests for 2 packages - metastudent and libgo
te in this thread if I
change them.
2016-07-14 10:32 GMT+03:00 merlettaia :
> Hi Andreas,
> I've added tests for 2 packages - metastudent and libgo-perl, which is
> used by metastudent and which produced error (patch in libgo-perl makes
> metastudent run work).
> BTW, I noticed t
Hi Andreas,
I fixed that reprof error and now it is ready for upload.
Alas, predictprotein still remains a problem :(
2016-07-14 10:51 GMT+03:00 Andreas Tille :
> [CC, ing other uploaders of reprof from rostlab]
> Hi Tanya,
>
> On Thu, Jul 14, 2016 at 10:32:44AM +0300, merlettaia w
Hi Andreas,
OK, I just wanted to write you about it:)
I also made small fix in proftmb and metastudent - turned on allow-stderr
restriction (both packaged failed in Debian CI server because of
pp-popularity-contest warning message output to stderr), they also worth
uploading.
You should also uploa
Hi Andreas,
2016-07-17 12:15 GMT+03:00 Andreas Tille :
>
> > You should also upload profbval (I've made changes after last upload, but
> > mention them in changelog in wrong place - now this is fixed).
>
> Upload as well.
>
> > I'll fix spelling warnings in libgo perl then.
>
> Fine.
>
Fixed.
Hi Andreas,
2016-07-17 22:20 GMT+03:00 Andreas Tille
>
>
> Feel free to "relax" with upgrading Pymol. ;-)
>
I'll work on it now.
--
Best wishes,
Tanya.
Good morning Andreas,
Check this patch, it should help.
It does the same thing as lapacke.patch (which is commented in
debian/patches/series file) - it adds a -llapack and -llapacke to LDLIBS in
src/Makefile. It also adds -lpthread - without it, this error appears
during compilation: "undefined re
Hi Andreas,
I've updated upstream version as described in Debian New Maintainer's
Guide, chapter 8.3 (
https://www.debian.org/doc/manuals/maint-guide/update.en.html#idp40812672)
Can you remember what problems you had during upstream update?
I had error message about conflict in libpng12-0 and libp
Hi Andreas,
For now I wrote simple test which runs over all .py and .pml scripts inside
specific directory and tries to run them with pymol with -c flag (for now
this script doesn't care if python errors appear during run - it only
checks that pymol closes as expected). This is made because some o
gt; > Andreas.
> > >
> > > On Wed, Jul 27, 2016 at 09:57:29PM +0200, Andreas Tille wrote:
> > > > Hi Tanya,
> > > >
> > > > I noticed you have created changelog entries for 1.8.2.1 so you seem
> to
> > > > have managed to u
Hi Andreas,
2016-08-17 10:57 GMT+03:00 Andreas Tille :
> Hi Tanya,
>
> On Tue, Aug 16, 2016 at 08:01:46PM +0300, merlettaia wrote:
> > Could you please take a look at pymol?
>
> I did now. I fixed some minor lintian issues (DEP3, override for
> spelling). I also
apbs.
2016-08-17 11:20 GMT+03:00 merlettaia :
> Hi Andreas,
>
> 2016-08-17 10:57 GMT+03:00 Andreas Tille :
>
>> Hi Tanya,
>>
>> On Tue, Aug 16, 2016 at 08:01:46PM +0300, merlettaia wrote:
>> > Could you please take a look at pymol?
>>
>> I did
fix debian/copyright now.
2016-08-17 10:57 GMT+03:00 Andreas Tille :
> Hi Tanya,
>
> On Tue, Aug 16, 2016 at 08:01:46PM +0300, merlettaia wrote:
> > Could you please take a look at pymol?
>
> I did now. I fixed some minor lintian issues (DEP3, override for
> spelling). I
se, I copied it as it is.
I've checked everything with cme fix dpkg-copyright.
2016-08-20 13:19 GMT+03:00 merlettaia :
> Hi Andreas,
> I've made testsuite for apbs (I took its own tests "(cd tests; python
> apbs_tester.py -c test_cases.cfg)", installed them to usr/sha
ed message --
From: Timothy Karl
Date: 2016-07-18 16:18 GMT+03:00
Subject: Re: on Debian "profphd' upstream ChangeLog's entry
To: merlettaia
Hi Tanya,
I checked back in my logs and found the following that I wrote on March 20,
2015, before the official release of Jessie:
It appears
Hi Michael and Andreas,
The maintainers have responded, now there is apbs-1.4.2 source archive on
SourceForge.
I'll check it tomorrow.
2016-08-22 22:38 GMT+03:00 Michael Banck :
> Hi,
>
> On Sat, Aug 20, 2016 at 01:19:03PM +0300, merlettaia wrote:
> > apbs source relea
or a day or two.
2016-08-21 13:21 GMT+03:00 merlettaia :
> Hi All,
> I've asked author of profphd changelog entry for details why profphd
> relies on older version of perl and perlbrew. His answer is given below.
> I'll try to fix profphd now - last time I tried to launch it wi
wrote unclear, but my flight is postponed for the second
time and it makes me little nervous. I described how I understand this
problem for now. I've also fixed small warning (several from other package
are left) and started to fix autopkgtest. For now basic tests should work
(I used profphd'
Hi All,
I’m writing you in case if someone has a small research
bioinformatics-related project to this academic term and wishes to find
some smart student (or students) to do it.
Our St.Petersburg’s local bioinformatics school (named Bioinformatics
Institute) provides 1-year study program in bioi
Hi Afif,
There is no need to apologize - It's ok.
I've told Bioinformatics Institute mentors about Debian Med Team and told
you about them. I think it would be good if you'll write them - to ensure
they'll mail you when they'll search for mentors next time, and it might
happen that you'll have eno
Hi Andreas, Charles, Nadiya and All!
2017-06-07 9:58 GMT+03:00 Andreas Tille :
> Hi Charles,
>
> thanks for the heads up.
>
> On Wed, Jun 07, 2017 at 07:28:18AM +0900, Charles Plessy wrote:
> > Hi Andreas,
> >
> > $ rmadison r-base
> > r-base | 2.15.1-4 | oldstable| source, all
Hi Andreas,
I would like to introduce you to another Outreachy internship candidate :)
Her name is Dana, she's a 1st year student of Chemoinformatics and
molecular modeling Master degree program at ITMO university [1]
Next year her study group is expected to study chemoinformatics at University
o
Hi All,
I plan to attend Recomb (http://recomb2018.fr/) next week.
Is there a chance to meet anyone there? Or maybe you could suggest me some
good places/laboratories worth visiting?
The only problem with me is, I don't speak or read French -.-
Regards,
Tanya Malygina.
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