Hej Martin and Dan! First of all, I wish you both a happy new year!
I have made the move to the BiocFileCache, but the build report (3.10 for easyRNASeq) fails as follows: * creating vignettes ... ERROR --- re-building ‘simpleRNASeq.Rmd’ using rmarkdown Quitting from lines 40-41 (./Chapters/01-Introduction.Rmd) Quitting from lines NA-42 (./Chapters/01-Introduction.Rmd) Error: processing vignette 'simpleRNASeq.Rmd' failed with diagnostics: bfcadd() failed; see warnings() I can’t reproduce it, so it seems to be related to the build system at Bioc? Thanks, Nico > On 25 Nov 2019, at 15:39, Martin Morgan <mtmorgan.b...@gmail.com> wrote: > > Thanks this seems like a problem with large file size on Windows, probably in > Rhtslib. > > It might be better practice and more reliable to use BiocFileCache for > downloads, e.g., > > url = > "ftp://ftp.plantgenie.org/Tutorials/RnaSeqTutorial/data/star/unitTest/213.1_subset_sortmerna_trimmomatic_sorted.bam.bai"; > BiocFileCache::bfcrpath(rnames = url) > > which downloads (once) and returns the path to the cached file. > > Martin > > On 11/25/19, 8:24 AM, "Bioc-devel on behalf of Nicolas Delhomme" > <bioc-devel-boun...@r-project.org on behalf of nicolas.delho...@umu.se> wrote: > > Hej! > > The easyRNASeq package is not building on tokay1, with what seems to be a > file decompression issue? > > > https://master.bioconductor.org/checkResults/3.10/bioc-LATEST/easyRNASeq/tokay1-buildsrc.html > > It works fine on the other OSs. > > The error is triggered while downloading a small dataset during the > vignette creation. I use `download.file` as the function to fetch the data, > so it should be cross-platform compatible. I have no easy access to a windows > machine, so I can’t easily reproduce the problem. Any insight into what could > be the reason would be much appreciated :-) > > The easy solution would be to turn off the evaluation of that section of > the vignette, but I’d rather not as it is a good test of the complete > functionality of the package (something that would feel ill-fitted as a unit > test). > > Thanks in advance, > > Nico > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
