[Bioc-devel] Symbolic links to ExperimentHub files on Windows
Hello all, My package is failing to build on Windows as one of the functions attempts to download files from ExperimentHub and then creates a directory with symbolic links to these files using R.utils::createLink. However, it seems on Windows that administrative privileges are required to create symbolic links. The downloaded files are a HDF5 file and corresponding RDS file for a HDF5-backed SummarizedExperiment object. The purpose of using symbolic links to them is so that a directory containing the links can be loaded using HDF5Array::loadHDF5SummarizedExperiment while leaving the downloaded files in the ExperimentHub cache. Without being able to create symbolic links to the files on Windows, the only alternatives I can think of are to move or copy the files from the cache into the SummarizedExperiment directory. Neither are ideal solutions as I would prefer not to move files out of the cache and since the files may be quite large I would also prefer to avoid copying them. If anyone has any other suggestions, I would really appreciate it. Best, Richard [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Package passing checks on Linux and macOS but failing on Windows
Okay thanks. However, I won't be able to fix my package until the dependencies are fixed. Is that okay? Cheers, Richard On Wed, 24 Apr 2024 at 15:45, Kern, Lori wrote: > Yes your package will still be included in the release. Even if a > package is failing, you would receive notifications and a deprecation cycle > before the package would be officially removed. We like to see package > fixed before a release so they can be made available to end users as soon > as possible and so that you as a maintainer would only need to fix one > branch instead of two. > > Cheers, > > Lori Shepherd - Kern > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > -- > *From:* Bioc-devel on behalf of > Richard Heery > *Sent:* Wednesday, April 24, 2024 7:35 AM > *To:* bioc-devel@r-project.org > *Subject:* [Bioc-devel] Package passing checks on Linux and macOS but > failing on Windows > > Hi all, > > My new package on the devel version of Bioconductor is passing the > build/check report on Linux and macOS, but failing on Windows (Palomino3). > It seems some other packages that my one depends on are also failing on > Windows (e.g. rtracklayer) so I am wondering will my package still be added > to the new release of Bioconductor if it is passing on Linux and macOS? > > Cheers, > > Richard > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > > https://secure-web.cisco.com/1t49XRTeE8loSvv35U4FnGrVHu50rpZSBti-9DZbr1dCqE7o0bVhKEtgut7wP5Bln-RhNML_v7MxZVe87WGSWbYYrSEj2oK_dA-EyXuxlAN9LcYbjH6NN5eXZC2MErWcdlAdPt6flPBvyWhPDnt-1lseoKgbfp9urTDU27vA05mMZaUY2DKn9M47U6uvKWOcmH26HIkl1aiKvWLWazCimKQYHyAHXYfEfNI0tReCKZNomnUK7KNy4AhGvSNLG6W9oPZvyKebITi7Qhr1vOlWrkFXbeTY51qGgsbvtojf0b3oVoE3TeKJzZ5_7DNfmwpZc/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-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
[Bioc-devel] Package passing checks on Linux and macOS but failing on Windows
Hi all, My new package on the devel version of Bioconductor is passing the build/check report on Linux and macOS, but failing on Windows (Palomino3). It seems some other packages that my one depends on are also failing on Windows (e.g. rtracklayer) so I am wondering will my package still be added to the new release of Bioconductor if it is passing on Linux and macOS? Cheers, Richard [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] R devel has skipped to 4.5?
Thanks Gábor, rig add next installed 4.4. Richard On Tue, 23 Apr 2024 at 12:04, Gábor Csárdi wrote: > The release candidate is R 4.4 currently. For Windows it is at > https://cran.r-project.org/bin/windows/base/rtest.html, for macos it > is at https://mac.r-project.org/ > > If you use rig (https://github.com/r-lib/rig), you can run > rig add next > which works on Windows, macOS and Linux > > G. > > On Tue, Apr 23, 2024 at 11:57 AM Richard Heery > wrote: > > > > I am trying to install the devel version of R, however it seems that now > on > > CRAN the current version is 4.3.3 while the devel version is 4.5 so I'm > not > > sure where I can find 4.4. > > > > [[alternative HTML version deleted]] > > > > ___ > > 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
[Bioc-devel] R devel has skipped to 4.5?
I am trying to install the devel version of R, however it seems that now on CRAN the current version is 4.3.3 while the devel version is 4.5 so I'm not sure where I can find 4.4. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] R version dependency
So the version of R depended on determines the version of Bioconductor that the BBS will use when testing the package? On Tue, 23 Apr 2024 at 04:41, Anatoly Sorokin wrote: > Hi, > You can even set 3.5 if your code working with that version of R, but > BiocManager won't load the latest Bioconductor version (3.19) unless you > have R 4.4. > > Cheers, > Anatoly > > On Tue, Apr 23, 2024 at 2:57 AM Richard Heery > wrote: > >> Hi all, >> >> I'm wondering what we should now list as the R version in the Depends >> section of the description file: the current version 4.3.3 or the >> development version 4.4? >> >> Cheers, >> >> Richard >> >> [[alternative HTML version deleted]] >> >> ___ >> 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
[Bioc-devel] R version dependency
Hi all, I'm wondering what we should now list as the R version in the Depends section of the description file: the current version 4.3.3 or the development version 4.4? Cheers, Richard [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Single Package Builder failing to detect subscription to the Bioc-devel mailing list
Hi all, My package submission is repeatedly failing due to an error saying I am not subscribed to the Bioc-devel mailing list, even though I am subscribed using this email. This is the same email I have in the DESCRIPTION file and also as my git user.email both globally and locally in the repository. Any ideas what could be causing this? Cheers, Richard [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Maximum allowed cores on Bioconductor Build System?
Hi all, I am wondering if there is a maximum allowed number of cores that can be used when building a vignette on the Bioconductor Build System? I make use of parallel computing in one of my vignettes, but if I don't use enough cores, it takes too long to build the vignette and I get a timeout error. Currently, I am just using BiocParallel::bpparam() to automatically choose the parallel backend in the vignette. Cheers, Richard [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Vignette files causing package to exceed 5 MB size limit
Hi all, My package tarball is only 4.4 MB when I build it without building the vignettes. However, it increases to 7 MB when I build the vignettes. My vignette is a html_document that creates several images and is 3.8 MB uncompressed so quite large. Since my package is under the 5 MB limit without building vignettes, would that be considered small enough to pass or must the size of the vignettes be counted as part of the package size? Cheers, Richard [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Use of master vs devel branch on g...@git.bioconductor.org
Hi all, I have a package in review on g...@git.bioconductor.org and I have added a remote named upstream pointing to my package there as outlined here http://contributions.bioconductor.org/git-version-control.html#new-package-workflow . However, I've noticed that there are two branches on the remote now, master and devel, and that I can push to the master branch okay, but if I push to the devel branch I get the error: src refspec devel does not match any error: failed to push some refs to 'g...@git.bioconductor.org: packages/TumourMethData.git'. I am unsure if I should continue using the master branch or not as all the examples in the linked workflow show use of the devel branch. Cheers, Richard [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
