[Bioc-devel] daily build failures for the trena package, related to BSgenome.Hsapiens.UCSC.hg38 2bit file

[Martin Morgan]

I tried to reproduce the commands reported by the build system. So on a fresh git clone

  $ cd /tmp
  $ git clone git using git.bioconductor.org:packages/trena
  $ R -vanilla CMD build --keep-empty-dirs --no-resave-data trena

(the buld system doesn't use vanilla, but I have an ~/.Rprofile and maybe other things, and I'm doing my best not to introduce extraneous stuff). I then tried to check as the build system does

R --vanilla CMD check --install=check:trena.install-out.txt --library=/Users/ma38727/bin/R-3-6-branch/library --no-vignettes --timings trena_1.7.1.tar.gz

where I tried various arguments for --library (an empty directory; the directory shown here which is the location my R is installed; the directory where my non-base R packages are installed, the current directory, the directory containing trena source, :-separated directories). I'd end up either with

* checking whether package ‘trena’ can be installed ... ERROR
Installation failed.
See ‘/private/tmp/trena.Rcheck/00install.out’ for details.
* DONE

or (if 'trena.install-out.txt' didn't exist in the cwd)

* checking whether package ‘trena’ can be installed ... ERROR
install log ‘’ does not exist
* DONE

I couldn't find helpful documentation (other than R CMD check --help) on what value --library= should take; maybe Hervé or other build system wiz can provide guidance so that we can exactly reproduce what the build system is doing?

I doubt any of the following is the magic bullet, but...

When I built and checked this on my local machine I received a warning and then error

* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘BSgenome.Scerevisiae.UCSC.sacCer3’
...
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:

  1 Test Suite :
  trena RUnit Tests - 87 test functions, 1 error, 0 failures
  ERROR in test_findMatchesByChromosomalRegion.yeast: Error in loadNamespace(name) :
    there is no package called 'BSgenome.Scerevisiae.UCSC.sacCer3'

because 'BSgenome.Scerevisiae.UCSC.sacCer3' is not listed in the Suggests: field of your package; are there other missing dependencies?

In the build report, it's weird to see 

[1] --- test_createGeneModelFromRegulatoryRegions
Called from: test_createGeneModelFromRegulatoryRegions()
Browse[1]> debug: checkTrue(nrow(tbl.geneModel) > 40)

which suggests that there is a stray browser() call in your code

$ grep -r browser *
...
inst/misc/multiModels/aqp4.R:  browser()
inst/misc/multiModels/aqp4.R:   browser()
inst/misc/multiModels/aqp4.R:   browser()
inst/misc/multiModels/aqp4-multi.R:  browser()
inst/misc/multiModels/aqp4-multi.R:   browser()
inst/misc/multiModels/aqp4-multi.R:   browser()
inst/misc/multiModels/aqp4-multi.R:   browser()
inst/misc/multiModels/aqp4-multi.R:   browser();
inst/unitTests/test_Trena.R:    browser()
inst/utils/evaluateAllSolvers.R:    browser()
inst/utils/TReNA.R:    browser()

In trena.Rcheck/tests/runTests.Rout

I see 

[1] --- test_scalePredictorPenalties.lasso
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
...
[1] --- test_scalePredictorPenalties.lasso
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix

i.e., the same test running twice. Why is that?

I notice that there are .DS_store files in your repository that shouldn't be there

trena master$ find . -name ".*"
.
./man/.DS_Store
./.Rbuildignore
./.gitignore
./.git
./inst/misc/.DS_Store
./inst/.DS_Store
./inst/demos/.DS_Store

Maybe resolving some of these issues, especially the last, helps to resolve problems?

Martin

On 5/22/19, 2:34 PM, "Bioc-devel on behalf of Paul Shannon" <bioc-devel-bounces using r-project.org on behalf of paul.thurmond.shannon using gmail.com> wrote:

    I get daily R CMD check failures visible at
    
      https://master.bioconductor.org/checkResults/3.9/bioc-LATEST/trena/malbec2-checksrc.html
    
    The recurring failure, which I cannot replicate on my own systems, is due to this error:
    
    test_.getScoredMotifs Warning in .seqlengths_TwoBitFile(x) : mustOpen: 
    
    Can't open /home/biocbuild/bbs-3.9-bioc/R/library/BSgenome.Hsapiens.UCSC.hg38/extdata/single_sequences.2bit to read: No such file or directory
    
    
    If this is my error, I’d be glad to fix it - though I will need some guidance on how to do so.
    
    Thank you,
    
     - Paul
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