Re: [Bioc-devel] Problem with uncompressing files on tokay1?
With some additional investigation this appears to be a firewall issue as the error was reproducible on other machines. Work is being done to rectify the issue. Get Outlook for Android<https://aka.ms/ghei36> From: Bioc-devel on behalf of Nicolas Delhomme Sent: Monday, January 20, 2020 4:43:11 AM To: Martin Morgan Cc: Dan Tenenbaum Subject: Re: [Bioc-devel] Problem with uncompressing files on tokay1? 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 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" > 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 This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Problem with uncompressing files on tokay1?
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 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" > 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
Re: [Bioc-devel] Problem with uncompressing files on tokay1?
Could this be another instance where you need to specify mode = "wb" when you call download.file()? I've seen many examples of Windows downloads being corrupted because it uses mode = "w" by default. Presumably BiocFileCache would both handle this correctly and save multiple downloads, so it's a double win. On Mon, 25 Nov 2019 at 15:40, Martin Morgan 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 > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Problem with uncompressing files on tokay1?
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" 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
[Bioc-devel] Problem with uncompressing files on tokay1?
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
