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 | user time
----------------------------------------------------------------------------------
libatlas-base-dev | Successful run | 11m24.204s
libopenblas-dev | Successful run | 10m31.860s
libblas-dev+liblapack-dev | Successful run | 10m34.368s
It seems that libatlas-base-dev is less effective, but I'm not sure if we
should exclude it from Depends, so I left if for now
On Tue, Mar 28, 2017 at 11:29 PM, Andreas Tille <andr...@an3as.eu> wrote:
> [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 TGAAAACGA 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 nucleotides and
> make
> > sense regarding specifics of DNA damage.
> >
> > 2) But even after fixing (1) I still got an error (log attached). The
> > problem is that on given dataset from pe_test mapdamage produces data
> with
> > NaNs and then tries to compute quantiles on this data. I think that on
> real
> > date NaNs also could be produced, so I treated this issue as a bug and
> made
> > a patch which changes the way how quantiles are computed --- now it
> removes
> > NaNs [1]
> >
> > 3) I wrote about all this to upstream as a comments to earlier created
> > issue and asked if it's really was a bug in their opinion
> >
> > 4) FInally, move forward to fixing mapdamage test suite
>
> Pretty good job. That's exactly the contribution I'm envisioning for the
> Outreachy project. I've just added the URL of the upstream issue to the
> patch.
>
> > 11: stop("missing values and NaN's not allowed if 'na.rm' is FALSE")
> > 10: quantile.default(newX[, i], ...)
> > 9: FUN(newX[, i], ...)
> > 8: apply(X, 1, quantile, c(0.025))
> > 7: data.frame(x = 1:nrow(da), pos = da[, "Pos"], mea = apply(X,
> > 1, mean), med = apply(X, 1, median), loCI = apply(X, 1, quantile,
> > c(0.025)), hiCI = apply(X, 1, quantile, c(0.975)))
> > 6: calcSampleStats(da, CTs)
> > 5: postPredCheck(dat, mcmcOut)
> > 4: eval(expr, envir, enclos)
> > 3: eval(ei, envir)
> > 2: withVisible(eval(ei, envir))
> > 1: source(paste(path_to_mapDamage_stats, "main.R", sep = ""))
> > The Bayesian statistics program failed to finish
> > Traceback (most recent call last):
> > File "/usr/local/bin/mapDamage", line 382, in <module>
> > sys.exit(main())
> > File "/usr/local/bin/mapDamage", line 365, in main
> > mapdamage.rscript.run_stats(options)
> > File "/usr/local/lib/python2.7/dist-packages/mapdamage/rscript.py",
> line 144, in run_stats
> > raise e
> > subprocess.CalledProcessError: Command '['Rscript',
> '/usr/local/lib/python2.7/dist-packages/mapdamage/Rscripts/stats/runGeneral.R',
> '--args', '30', '10000', '10', '50000', '0', '0', '1', '1', '0', '0', '1',
> '12', 'results_pe/',
> '/usr/local/lib/python2.7/dist-packages/mapdamage/Rscripts/stats/',
> 'results_pe/Stats_out', '0', '0', '0', 'results_pe/acgt_ratio.csv', '0',
> '0']' returned non-zero exit status 1
>
> I'd recommend to manually run this script.
>
> Did you do some investigation what dependency providing liblapack.so and
> libblas.so are needed (see my mail from yesterday)?
>
> Kind regards
>
> Andreas.
>
> --
> http://fam-tille.de
>
>
