[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
