R package CI test failures
Hello
I had a look at which packages are have long-term test failures on
debian CI [1]. This list doesn't include failures only on arm64, or
those for which the tests have recently passed and are perhaps random
failures.
At least half of the failing packages appear to fail for trivial and
hopefully easily fixable reasons*. Cleaning these up would make it
easier to spot the failures which actually point to interesting regressions.
*(these might of course be masking more complex issues)
Commonly encountered issues:
missing-dep - extra packages needed for test - usually
r-cran-runit/r-cran-testthat
non-lowercased path for vignette: output contains something like "cannot
stat /usr/share/doc/r-bioc-biovizBase/examples/vignettes/*"
bad substitution in run-unit-test: output contains something like
"cannot stat /usr/share/doc/r-bioc-cumme[bund/examples/vignettes/*"
min_overlap_score bug: several have errors about "object
min_overlap_score not found" - possibly a real version mismatch bug?
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
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
r-bioc-biocinstaller: missing dep r-bioc-biocgenerics
r-bioc-biomart: bad substitution in run-unit-test
r-bioc-biovizbase: non-lowercased path for vignette
r-bioc-bsgenome: non-lowercased path for vignette
r-bioc-cummerbund: bad substitution in run-unit-test
r-bioc-genefilter: missing dep r-cran-class
r-bioc-genomicalignments: min_overlap_score bug
r-bioc-genomicranges: min_overlap_score bug
r-bioc-hilbertvis: non-lowercased path for vignette
r-bioc-limma: ?
r-bioc-rsamtools: missing dep r-cran-runit
r-bioc-snpstats: non-lowercased path for vignette
r-bioc-summarizedexperiment: missing dep r-cran-runit
r-bioc-variantannotation: min_overlap_score bug
# r-cran
r-cran-adegraphcis: missing dep spdep (unpackaged?)
r-cran-afex: ?
r-cran-bayesfactor: missing dep r-cran-testthat
r-cran-bbmisc: missing dep r-cran-codetools
r-cran-bms: non-lowercased path for vignette
r-cran-cmprsk: ?
r-cran-contfrac: tries to test r-cran-elliptic
r-cran-doparallel: ?
r-cran-dplyr: R version mismatch (built under 3.3.0)
r-cran-epi: missing dep r-cran-plyr
r-cran-etm: tries to test r-cran-cmprsk
r-cran-evaluate: ?
r-cran-futile.logger: error in run-unit-test script
r-cran-ggplot2: error in run-unit-test script
r-cran-htmltools: missing dep on r-cran-rcpp
r-cran-hypergeo: error in run-unit-test script
r-cran-lambda.r: error in run-unit-test script
r-cran-learnbayes: non-lowercased path for vignette
r-cran-magrittr: error in run-unit-test script
r-cran-plyr: error in run-unit-test script
r-cran-qtl: missing dep r-cran-testthat
r-cran-r.methodss3: bad subsitution in run-unit-test
r-cran-r.utils: error in run-unit-test
r-cran-r6: tries to test r-cran-rncl
r-cran-rncl: missing dep r-cran-rcpp
r-cran-rocr: ?
r-cran-shiny: missing dep r-cran-ggplot2
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
Gordon
[1]: https://ci.debian.net/packages/r/
Beware that debian-CI still lists packages as failed for which the test
was removed years ago - eg, r-bioc-annotationdbi (last test 2014) -
hopefully I removed all of these from the list
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