Bug#848326: Outreachy 2017 (Round 14)

[Nadiya Sitdykova]

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 linker
call, I saved that log so it's attached

3) Done

On Mon, Mar 27, 2017 at 2:03 PM, Andreas Tille  wrote:

> 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
> >   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 absence of gsl-config.
>
> Do you want to say that after installing r-cran-rcppgsl on a clean
> system is not able to run the test suite of r-cran-rcppgsl itself and
> the installation of gsl-config is required to do so?
>
> Or is it rather that gsl-config is required to run the test suite of
> mapdamage?
>
> > So I've
> > done some googling, installed gsl-devel and it helped with
> > run-r-packages-check but I still didn't get the same error for
> > run-unit-test as you, I got:
> >
> > Compilation ERROR, function(s)/method(s) not created! /usr/bin/ld:
> > cannot find -llapack
> > /usr/bin/ld: cannot find -lblas
>
> Hmmm, at what point of the test is the linker ld called?
>
> > So I also installed libopenblas-base and libopenblas-dev. NOW I got the
> > same error as you.
>
> I wonder in how far the development package is needed in the test suite.
> May be it would be enlightening if you always would write down the
> command you called and add a larger chunk of the resulting output.
>
> As you describe things it seems this is another missing dependency.
>
> > I looked into it, and it seems that the problem is that
> > in the test data nucleotide frequency array looks like 0.556
> 0.222
> > 0.222 0,
> > i.e. frequence for T is zero, which is not what expected by mapdamage
> from
> > line 4 in
> > https://github.com/ginolhac/mapDamage/blob/master/
> mapdamage/Rscripts/stats/function.R#L4
> > Even though documentation doesn't say that zero frequences are not
> allowed.
> >
> > I changed reference file from "CGAGGGCGA" to "TGCGA" (so all
> frequences
> > > 0) and now it executes without errors.
>
> Would you mind reporting this in the upstream issue tracker?
>
> Thanks for your patient work on this
>
>Andreas.
>
> --
> http://fam-tille.de
>
>


run-unit-test.out
Description: Binary data

Bug#848326: Outreachy 2017 (Round 14)

[Andreas Tille]

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
>   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 absence of gsl-config.

Do you want to say that after installing r-cran-rcppgsl on a clean
system is not able to run the test suite of r-cran-rcppgsl itself and
the installation of gsl-config is required to do so?

Or is it rather that gsl-config is required to run the test suite of
mapdamage?

> So I've
> done some googling, installed gsl-devel and it helped with
> run-r-packages-check but I still didn't get the same error for
> run-unit-test as you, I got:
> 
> Compilation ERROR, function(s)/method(s) not created! /usr/bin/ld:
> cannot find -llapack
> /usr/bin/ld: cannot find -lblas

Hmmm, at what point of the test is the linker ld called?
 
> So I also installed libopenblas-base and libopenblas-dev. NOW I got the
> same error as you.

I wonder in how far the development package is needed in the test suite.
May be it would be enlightening if you always would write down the
command you called and add a larger chunk of the resulting output.

As you describe things it seems this is another missing dependency.

> I looked into it, and it seems that the problem is that
> in the test data nucleotide frequency array looks like 0.556 0.222
> 0.222 0,
> i.e. frequence for T is zero, which is not what expected by mapdamage from
> line 4 in
> https://github.com/ginolhac/mapDamage/blob/master/mapdamage/Rscripts/stats/function.R#L4
> Even though documentation doesn't say that zero frequences are not allowed.
> 
> I changed reference file from "CGAGGGCGA" to "TGCGA" (so all frequences
> > 0) and now it executes without errors.

Would you mind reporting this in the upstream issue tracker?
 
Thanks for your patient work on this

   Andreas.

-- 
http://fam-tille.de

Bug#848326: Outreachy 2017 (Round 14)

[Nadiya Sitdykova]

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 absence of gsl-config. So I've
done some googling, installed gsl-devel and it helped with
run-r-packages-check but I still didn't get the same error for
run-unit-test as you, I got:

Compilation ERROR, function(s)/method(s) not created! /usr/bin/ld:
cannot find -llapack
/usr/bin/ld: cannot find -lblas

So I also installed libopenblas-base and libopenblas-dev. NOW I got the
same error as you. I looked into it, and it seems that the problem is that
in the test data nucleotide frequency array looks like 0.556 0.222
0.222 0,
i.e. frequence for T is zero, which is not what expected by mapdamage from
line 4 in
https://github.com/ginolhac/mapDamage/blob/master/mapdamage/Rscripts/stats/function.R#L4
Even though documentation doesn't say that zero frequences are not allowed.

I changed reference file from "CGAGGGCGA" to "TGCGA" (so all frequences
> 0) and now it executes without errors.

Regards, Nadiya

On Sun, Mar 26, 2017 at 11:40 PM, Andreas Tille  wrote:

> 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 Sun, Mar 26, 2017 at 1:25 PM, Andreas Tille  wrote:
> > >
> > >  LANG=C . run-unit-test 2>&1 | tee > run-unit-test.out
> > >
> > > I get the attached build log - but this does not contain the string
> > > Rcpp.  This needs to be investigated.
>
> It really seems that your r-cran-rcppgsl installation is broken.  You
> might like to try
>
>   apt-get source r-cran-rcppgsl
>   LC_ALL=C R --no-save < r-cran-rcppgsl*/tests/doRUnit.R
>
> to make sure this R module works properly.  I admit I have not
> experienced severy problems with R modules on clean Debian systems.
>
> Once we get r-cran-rcppgsl working properly you will probably get the
> same errors as I observed.
>
> Kind regards
>
>   Andreas.
>
> --
> http://fam-tille.de
>
>

Bug#848326: Outreachy 2017 (Round 14)

[Andreas Tille]

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 Sun, Mar 26, 2017 at 1:25 PM, Andreas Tille  wrote:
> >
> >  LANG=C . run-unit-test 2>&1 | tee > run-unit-test.out
> >
> > I get the attached build log - but this does not contain the string
> > Rcpp.  This needs to be investigated.

It really seems that your r-cran-rcppgsl installation is broken.  You
might like to try

  apt-get source r-cran-rcppgsl
  LC_ALL=C R --no-save < r-cran-rcppgsl*/tests/doRUnit.R

to make sure this R module works properly.  I admit I have not
experienced severy problems with R modules on clean Debian systems.

Once we get r-cran-rcppgsl working properly you will probably get the
same errors as I observed.

Kind regards

  Andreas.

-- 
http://fam-tille.de