Re: CI for mapdamage (Was: Outreachy 2017 (Round 14))

Hi Nadiya, On Wed, Mar 29, 2017 at 06:36:41PM -0700, Nadiya Sitdykova wrote: > I uncommented all tests in run-unit-test and now they work perfectly fine > so I closed the bug #848326 inside changelog > Also I added some info to README.test, which I think could be useful for > users Thanks for

Re: CI for filo (Was: Outreachy 2017 (Round 14))

Hello Andreas, I will ask for this before me you mention i will go on another bug. Thanks for reply. Best Regards 2017-03-30 10:41 GMT+03:00 Andreas Tille : > retitle 848335 Filo should be removed from Debian after Stretch release > since it is unmaintained and can be

Re: CI for filo (Was: Outreachy 2017 (Round 14))

retitle 848335 Filo should be removed from Debian after Stretch release since it is unmaintained and can be replaced thanks Hi Charles, thanks for your explanation. On Thu, Mar 30, 2017 at 10:54:14AM +0900, Charles Plessy wrote: > Le Wed, Mar 29, 2017 at 08:37:28AM +0200, Andreas Tille a écrit

Re: CI for filo (Was: Outreachy 2017 (Round 14))

Le Wed, Mar 29, 2017 at 08:37:28AM +0200, Andreas Tille a écrit : > > In principle the best idea would be to convince upstream to choose less > generic names but I think development of filo is stalled. Hi all, indeed the development of filo is stalled. Filo contains three binaires:

Re: CI for mapdamage (Was: Outreachy 2017 (Round 14))

Hello Andreas, I uncommented all tests in run-unit-test and now they work perfectly fine so I closed the bug #848326 inside changelog Also I added some info to README.test, which I think could be useful for users Regards, Nadiya On Wed, Mar 29, 2017 at 2:48 PM, Nadiya Sitdykova

Re: CI for mapdamage (Was: Outreachy 2017 (Round 14))

Hello Andreas, >Did you do some investigation what dependency providing liblapack.so and >libblas.so are needed (see my mail from yesterday)? Yes, I tried to run the test with different packages installed, and here are results: packages| result|

CI for filo (Was: Outreachy 2017 (Round 14))

[Changing subject to split the two competing topics] Hi Büşra, On Wed, Mar 29, 2017 at 12:56:40AM +0300, Canberk Koç wrote: ^^^ :-) > I was working on filo and find out something. Filo binaries goes to > /usr/lib/filo section and i think it is

CI for mapdamage (Was: Outreachy 2017 (Round 14))

[Changed subject to split up to topics in one thread] Hi Nadiya, On Tue, Mar 28, 2017 at 10:23:00PM -0700, Nadiya Sitdykova wrote: > 1) I read the paper about mapdamage and figured out that with given pe.sam > file the reference TGCGA wouldn't make sense as the particular type of >

Re: Outreachy 2017 (Round 14)

Hello Andreas, 1) I read the paper about mapdamage and figured out that with given pe.sam file the reference TGCGA wouldn't make sense as the particular type of substitutions is specific for ancient DNA damages. So further for tests I used reference CGATACGA -- which contains all types of

Re: Outreachy 2017 (Round 14)

Hello Andreas, 1) Actually I was wrong, after changing reference to TGCGA the new type of error arises, so I'm working on it for now 2) I created an issue here https://github.com/ginolhac/mapDamage/issues/18 Regards, Nadiya On Tue, Mar 28, 2017 at 2:58 PM, Büşra Selin Pekişçi <

Re: Outreachy 2017 (Round 14)

Hello Andreas, Sorry for wrong mail from Canberk's mail account.I was using his computer and missend mail from his account. 2017-03-29 0:56 GMT+03:00 Canberk Koç : > Hello Andreas, > > I was working on filo and find out something. Filo binaries goes to > /usr/lib/filo

Re: Outreachy 2017 (Round 14)

Hello Andreas, I was working on filo and find out something. Filo binaries goes to /usr/lib/filo section and i think it is wrong . They make these changes because binary names are too generic should i make link them to bin directory with filo-* like name ? Best Regards Canberk Koç [image:

Re: Outreachy 2017 (Round 14)

Hi Büşra, On Tue, Mar 28, 2017 at 10:49:30PM +0300, Büşra Selin Pekişçi wrote: > I check Prank git and find out something i don't know if it is important. > At run-unit-test script you make a trap and give there $ADTTMP variable can > we use it instead of $AUTOPKGTEST_TMP variable. No. :-) > I

Re: Outreachy 2017 (Round 14)

Hello Andreas, I check Prank git and find out something i don't know if it is important. At run-unit-test script you make a trap and give there $ADTTMP variable can we use it instead of $AUTOPKGTEST_TMP variable.I was curious about it . And i start to work on filo package for your information .

Re: Outreachy 2017 (Round 14)

Hi Nadiya, On Mon, Mar 27, 2017 at 02:52:25PM -0700, Nadiya Sitdykova wrote: > 1) Yes, I mean after I tried > > apt-get source r-cran-rcppgsl > LC_ALL=C R --no-save < r-cran-rcppgsl*/tests/doRUnit.R > > There was an error "gsl-config not found". Unfortunately, I didn't save > that log and

Re: Outreachy 2017 (Round 14)

1) Yes, I mean after I tried apt-get source r-cran-rcppgsl LC_ALL=C R --no-save < r-cran-rcppgsl*/tests/doRUnit.R There was an error "gsl-config not found". Unfortunately, I didn't save that log and can't reproduce it now =( 2) I executed autopkgtest . -- null and run-unit-test failed after

Re: Outreachy 2017 (Round 14)

Hi Nadiya, thanks for your patience. It seems we have spotted here a really buggy package with missing dependencies. On Mon, Mar 27, 2017 at 01:20:30PM -0700, Nadiya Sitdykova wrote: > Here is the output of apt-cache policy r-cran-rcppgsl: > > r-cran-rcppgsl: > Installed: 0.3.2-1 >

Re: Outreachy 2017 (Round 14)

Here is the output of apt-cache policy r-cran-rcppgsl: r-cran-rcppgsl: Installed: 0.3.2-1 Candidate: 0.3.2-1 Version table: *** 0.3.2-1 500 500 http://ftp.us.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status tests for r-cran-rcppgsl crashed because of

Re: Outreachy 2017 (Round 14)

Hi Nadiya, On Sun, Mar 26, 2017 at 02:31:47PM -0700, Nadiya Sitdykova wrote: > I generated output files for run-unit-test and run-r-packages-check the > exact same way you described. Regarding run-r-package-check.out. Could you please post the result of apt-cache policy r-cran-rcppgsl > On

Re: Outreachy 2017 (Round 14)

Hello Andreas, I generated output files for run-unit-test and run-r-packages-check the exact same way you described. Regards, Nadiya On Sun, Mar 26, 2017 at 1:25 PM, Andreas Tille wrote: > Hello Nadiya, > > On Sat, Mar 25, 2017 at 08:31:24PM -0700, Nadiya Sitdykova wrote: >

Re: Outreachy 2017 (Round 14)

Hello Nadiya, On Sat, Mar 25, 2017 at 08:31:24PM -0700, Nadiya Sitdykova wrote: > Thank you for instructions for using dch, I hope now I got it right. I think so (except the blank line in the beginning which was probably a typo). > 1) I edited patch use_debian_packaged_seqtk.patch so I guess

Re: Outreachy 2017 (Round 14)

Hello Andreas, Thank you for instructions for using dch, I hope now I got it right. 1) I edited patch use_debian_packaged_seqtk.patch so I guess the problem with seqtk should be resolved now. 2) I have this error on Ubuntu xenial, Debian jessie and after you mentioned that it's better to use

Re: Outreachy 2017 (Round 14)

Hi Nadiya, thanks for your work on this. It seems you've hit a non-trival example but that's no problem but rather a challenge, right? At first I've fixed debian/changelog. It seems you always called dch -i which is for each call bumping the Debian release. Please use the -i option only

Re: Outreachy 2017 (Round 14)

Hello, I've added tests of examples from here https://ginolhac.github.io/mapDamage/#a5 But only two of them works fine. Other two "Cannot use -- with missing R-libraries", so it seems they need recommended r-cran-rcppgsl package. I created simple stand-alone test with this package in depends to

Re: Outreachy 2017 (Round 14)

Hello Büşra, On Thu, Mar 23, 2017 at 01:47:59AM +0300, Büşra Selin Pekişçi wrote: > I commit my work to git. Will move next bug . Thanks for help. Nice. :-) I've added some further changes, mainly * Installing the test script into the package and a documentation for users how they can

Re: Outreachy 2017 (Round 14)

Hello Andreas, I commit my work to git. Will move next bug . Thanks for help. Best Regards 2017-03-21 11:01 GMT+03:00 Andreas Tille : > On Tue, Mar 21, 2017 at 08:34:43AM +0100, Andreas Tille wrote: > > Since I have some experience with SVN to Git conversion I'll do so. > > >

Re: Outreachy 2017 (Round 14)

On Tue, Mar 21, 2017 at 08:34:43AM +0100, Andreas Tille wrote: > Since I have some experience with SVN to Git conversion I'll do so. > > I'll ping here once this is done Prank is now at https://anonscm.debian.org/git/debian-med/prank.git Have fun Andreas. -- http://fam-tille.de

Re: Outreachy 2017 (Round 14)

Hi Büşra, On Mon, Mar 20, 2017 at 11:36:32PM +0300, Büşra Selin Pekişçi wrote: > I recognize Prank package at SVN i am not familiar with SVN what should i > do ? Shall i look SVN or can somebody take package to Git. Thanks for help. Since I have some experience with SVN to Git conversion I'll do

Re: Outreachy 2017 (Round 14)

Hello Andreas, I recognize Prank package at SVN i am not familiar with SVN what should i do ? Shall i look SVN or can somebody take package to Git. Thanks for help. Best Regards. 2017-03-20 10:46 GMT+03:00 Andreas Tille : > Hi Büşra, > > On Sun, Mar 19, 2017 at 10:29:01PM

Re: Outreachy 2017 (Round 14)

Hi Büşra, On Sun, Mar 19, 2017 at 10:29:01PM +0300, Büşra Selin Pekişçi wrote: > I make request to participate Debian-Med at Alioth fyi. I accepted yesterday evening - just let us know here if you have problems commiting your changes. Thanks for your work on this Andreas. --

Re: Outreachy 2017 (Round 14)

Hello Andreas, I make request to participate Debian-Med at Alioth fyi. Best Regards. 2017-03-17 23:46 GMT+03:00 Andreas Tille : > Hi Büşra > > On Fri, Mar 17, 2017 at 11:21:44PM +0300, Büşra Selin Pekişçi wrote: > > I made a testsuite for bug number #848329 > >

Re: Outreachy 2017 (Round 14)

Hello All, I made a testsuite for bug number #848329 . I look at program's website and there is no documentation so i made a simple test by looking examples. Now what should i do to commit code to you ? Thanks for help. Regards *Büşra

Re: Outreachy 2017 (Round 14)

Hello Again, I pick this bug in a random way and did not see somebody working on it sorry. So i can take another bug :) I am reading the policy and keep in touch with Canberk .He mentioned me about alioth and packaging basics will help me on the progress. Thanks for help Regards 2017-03-16

Re: Outreachy 2017 (Round 14)

Hi Nadiya, On Wed, Mar 15, 2017 at 05:37:58PM -0700, Nadiya Sitdykova wrote: > I've already been working on this bug for some time. Maybe it's ok if we > both will work on it, but I decided just to notify if it's not ok. Good point. I forgot to check the numbers. I guess its better if

Re: Outreachy 2017 (Round 14)

Hi all! I've already been working on this bug for some time. Maybe it's ok if we both will work on it, but I decided just to notify if it's not ok. On Wed, Mar 15, 2017 at 3:03 PM, Andreas Tille wrote: > Hello Büşra, > > thanks for your interest in Debian Med. > > On Thu, Mar

Re: Outreachy 2017 (Round 14)

Hello Büşra, thanks for your interest in Debian Med. On Thu, Mar 16, 2017 at 12:45:54AM +0300, Büşra Selin Pekişçi wrote: > I am Busra from Turkey. I am studying Computer Engineering at Çanakkale 18 > Mart University. I saw the Debian-Med idea at Outreachy organization's list > and my friend

Outreachy 2017 (Round 14)

Hello Andreas, I am Busra from Turkey. I am studying Computer Engineering at Çanakkale 18 Mart University. I saw the Debian-Med idea at Outreachy organization's list and my friend Canberk told me about his experience on GSOC last year. I want to participate Outreachy so i am looking at bug 84326