I tried to reproduce the commands reported by the build system. So on a fresh
git clone
$ cd /tmp
$ git clone g...@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-boun...@r-project.org on behalf of paul.thurmond.shan...@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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