Re: R package CI test failures
[Jonathon, please seek for your name in the text below.]
Hi Gordon,
thanks a lot for your effort about testing R packages.
On Wed, Apr 27, 2016 at 12:00:05PM +0200, Gordon Ball wrote:
>
> non-lowercased path for vignette: output contains something like "cannot
> stat /usr/share/doc/r-bioc-biovizBase/examples/vignettes/*"
Since I seem to fail the actual reason for this one. Could someone
please correct me that this code
oname=biovizBase
pkg=r-bioc-`echo $oname | tr [A-Z] [a-z]`
(https://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-biovizbase/trunk/debian/tests/run-unit-test?view=markup)
should ensure lower cased package name? I received a similar report
like you mention above but I totally fail to understand the issue
behind it - perhaps another pair of eyes looking at it might enlight
me. My only idea is to rather use
pkg=r-bioc-`echo $oname | tr '[A-Z]' '[a-z]'`
and so I try this even if I think this is equivalent.
> bad substitution in run-unit-test: output contains something like
> "cannot stat /usr/share/doc/r-bioc-cumme[bund/examples/vignettes/*"
That's even more strange. I like to just insert the original CRAN
spelling and calculate the Debian package from mit but tr does not
seem to do a reliable job and I wonder why.
> tries to test r-cran-whatever: looks like a copy-paste error in
> run-unit-test, tries to run a different package's test suite
Ahhh, I'd happily get rid of cut-n-pastos.
> error in run-unit-test: appears to be a bug in the shell script (bad
> find arguments, etc)
>
> ?: not obvious what went wrong - might be a true positive
>
> # r-bioc
>
> r-bioc-aroma.light: attempts install.packages
I don't understand this one.
> r-bioc-biocinstaller: missing dep r-bioc-biocgenerics
Fixed in recent upload.
> r-bioc-biomart: bad substitution in run-unit-test
Uploaded new version with quotes in tr call.
> r-bioc-biovizbase: non-lowercased path for vignette
> r-bioc-bsgenome: non-lowercased path for vignette
Waiting for confirmation that quotes in tr call are helpful.
> r-bioc-cummerbund: bad substitution in run-unit-test
Uploaded new version with quotes in tr call.
> r-bioc-genefilter: missing dep r-cran-class
Fixed in recent upload of new upstream version.
> r-bioc-genomicalignments: min_overlap_score bug
> r-bioc-genomicranges: min_overlap_score bug
I don't understand this type.
> r-bioc-hilbertvis: non-lowercased path for vignette
Waiting for confirmation that quotes in tr call are helpful.
> r-bioc-limma: ?
?
> r-bioc-rsamtools: missing dep r-cran-runit
Fixed in recent upload
> r-bioc-snpstats: non-lowercased path for vignette
Waiting for confirmation that quotes in tr call are helpful.
> r-bioc-summarizedexperiment: missing dep r-cran-runit
Fixed in recent upload of new version.
> r-bioc-variantannotation: min_overlap_score bug
I don't understand this type.
> # r-cran
>
> r-cran-adegraphcis: missing dep spdep (unpackaged?)
Grrr, I'm fighting for r-cran-spdep since years (#752876) and its again
in new. If you want to help please review the copyright and convince
ftpmaster that it is free.
> r-cran-afex:
?
> r-cran-bayesfactor: missing dep r-cran-testthat
Fixed in recent team upload (Jonathon, please git pull)
> r-cran-bbmisc: missing dep r-cran-codetools
Fixed in recent upload
> r-cran-bms: non-lowercased path for vignette
Waiting for confirmation that quotes in tr call are helpful.
(Jonathon, feel free to beat me with a fix!)
> r-cran-cmprsk: ?
?
> r-cran-contfrac: tries to test r-cran-elliptic
Jonathon, please fix.
> r-cran-doparallel: ?
?
> r-cran-dplyr: R version mismatch (built under 3.3.0)
Huhu, what's that???
> r-cran-epi: missing dep r-cran-plyr
Fixed in recent upload (missing Dependency in package)
> r-cran-etm: tries to test r-cran-cmprsk
Fixed in recent upload
> r-cran-evaluate: ?
?
> r-cran-futile.logger: error in run-unit-test script
What kind of error? Runs fine for me if I call it directly.
> r-cran-ggplot2: error in run-unit-test script
Fixed in recent upload
> r-cran-htmltools: missing dep on r-cran-rcpp
Fixed in recent upload
> r-cran-hypergeo: error in run-unit-test script
Jonathon, please fix.
> r-cran-lambda.r: error in run-unit-test script
What kind of error? Runs fine for me if I call it directly.
> r-cran-learnbayes: non-lowercased path for vignette
Fixed in recent upload - hopefully Closes: #759413
> r-cran-magrittr: error in run-unit-test script
What kind of error? Runs fine for me if I call it directly.
> r-cran-plyr: error in run-unit-test script
Fixed in recent upload
> r-cran-qtl: missing dep r-cran-testthat
Fixed in recent upload of new upstream version
> r-cran-r.methodss3: bad subsitution in run-unit-test
Waiting for confirmation that quotes in tr call are helpful.
> r-cran-r.utils: error in run-unit-test
What kind of error? Runs fine for me if I call it directly.
> r-cran-r6: tries to test r-cran-rncl
Fixed by yourself in Git - possibly missing quotes in tr call.
> r-cran-rncl: missing dep r-cran-rcpp
Fixed in recent upload
> r-cran-rocr: ?
?
> r-cran-shiny: missing dep r-cran-ggplot2
Fixed in recent upload
> r-cran-sp: missing dep rgeos (unpackaged?)
> r-cran-surveillance: unsatisfyable dependencies
> r-cran-testthat: unsatisfyable dependencies
> r-cran-tidyr: R version mismatch (built under 3.3.0)
> r-cran-xml2: missing dep r-cran-rcpp
I'll leave the last 5 on my desk for tomorrow.
Thanks for your work on testing R packages
Andreas.
--
http://fam-tille.de
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