[Bioc-devel] Development branch build error from celda
Hi, I am the maintainer of Bioconductor package celda. Recently there is an build check error on the development branch specifically on Windows i386 platform. I cannot reproduce this error on my local x64 Windows machine. The error report is as follows: * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... ERROR Running examples in 'celda-Ex.R' failed Warning in file(con, "r") : cannot open file '../celda-Ex_i386.Rout': Permission denied Error in file(con, "r") : cannot open the connection Execution halted Does anyone have any idea about how I can fix this? Thanks, Zhe [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] EXTERNAL: Re: GO.db package data source
Yes - those are the scripts we are using. We (Martin and I) will be spending time tomorrow to work through this. With the release quickly approaching we will work on making edits to the scripts to download this new data. Thank you for bringing this to our attention. - Kayla On 4/1/20, 12:44 PM, "Bioc-devel on behalf of James W. MacDonald" wrote: Further to this point, when comparing to the latest OBO from geneontology, it looks like the current GO.db has just over 1000 GO IDs that are not in GO any longer, and almost 500 GO IDs are in the GO OBO file that are not in GO.db On Wed, Apr 1, 2020 at 12:11 PM James W. MacDonald wrote: > Are we still using the scripts in > BioconductorAnnotationPipeline/go/scripts to download GO data and create > the GO.db package? > > If so, that is likely a problem that will only get worse with time. > Apparently geneontology.org is no longer generating the SQL dumps that > the go scripts rely on, so whatever we download is outdated. There have > been some complaints to the helpdesk about the data ( > https://github.com/geneontology/helpdesk/issues/4), where they discuss a > new pipeline (RDF) that may not have ended up being the new pipeline? > > Apparently they are now using OBO or OWL ( > http://geneontology.org/docs/download-ontology/) for the downloadable > data, so we should consider switching. > > I bring this up because apparently the current release GO.db is missing > terms that were added as far back as 2018. > > Best, > > Jim > > > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 [[alternative HTML version deleted]] ___ 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. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] GO.db package data source
Further to this point, when comparing to the latest OBO from geneontology, it looks like the current GO.db has just over 1000 GO IDs that are not in GO any longer, and almost 500 GO IDs are in the GO OBO file that are not in GO.db On Wed, Apr 1, 2020 at 12:11 PM James W. MacDonald wrote: > Are we still using the scripts in > BioconductorAnnotationPipeline/go/scripts to download GO data and create > the GO.db package? > > If so, that is likely a problem that will only get worse with time. > Apparently geneontology.org is no longer generating the SQL dumps that > the go scripts rely on, so whatever we download is outdated. There have > been some complaints to the helpdesk about the data ( > https://github.com/geneontology/helpdesk/issues/4), where they discuss a > new pipeline (RDF) that may not have ended up being the new pipeline? > > Apparently they are now using OBO or OWL ( > http://geneontology.org/docs/download-ontology/) for the downloadable > data, so we should consider switching. > > I bring this up because apparently the current release GO.db is missing > terms that were added as far back as 2018. > > Best, > > Jim > > > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] GO.db package data source
Are we still using the scripts in BioconductorAnnotationPipeline/go/scripts to download GO data and create the GO.db package? If so, that is likely a problem that will only get worse with time. Apparently geneontology.org is no longer generating the SQL dumps that the go scripts rely on, so whatever we download is outdated. There have been some complaints to the helpdesk about the data ( https://github.com/geneontology/helpdesk/issues/4), where they discuss a new pipeline (RDF) that may not have ended up being the new pipeline? Apparently they are now using OBO or OWL ( http://geneontology.org/docs/download-ontology/) for the downloadable data, so we should consider switching. I bring this up because apparently the current release GO.db is missing terms that were added as far back as 2018. Best, Jim -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Problems caused by earlier Rhtslib migration
Hi Antti, On 3/30/20 00:14, Antti Honkela wrote: Hi all, I am a co-maintainer of BitSeq. About a year ago, we were offered help in migration from Rsamtools to Rhtslib and we took the offer. The commit pushed by BioC team added a file src/bam_plbuf.c with just one line: #include This is now making our Windows build fail because of an infinite include loop. As I don't understand why the file was added in the first place, help in resolving the issue would be appreciated! This is a trick to put a copy of the bam_plbuf.c file from the Rhtslib package in BitSeq/src/. I used the same trick for 7 other packages that I also migrated from Rsamtools to Rhtslib and it works fine on all platforms, including Windows. Not sure what's special about BitSeq on Windows. Can you please try to rename the file e.g. to Rhtslib_bam_plbuf.c? This should avoid the "include nested too deeply" error, hopefully. You might want to do the same thing for the sam.c file. Thanks, H. Best regards, Antti ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=uZWZ6Z8-kMo46tPlCV-srVxHQ6g2EjpgilOYFeyGxYw=LuTyhFobrvTJ5otx3h60JgLILxjQvqeXR4XC9xHdHEI= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Devel Builder Updates
We will be updating the devel builders to the lastest R 4.0.0 later today. This should not affect the daily builder but may interrupt the Single Package Builder for new submission. Build report status for a platform on the single package builder may be missing during the update period. The downtown should be brief. Thank you for your understanding. Cheers, Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 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] Problems with Biocredentials
Hi,
Did you add your Github username to your BiocCredentials account?
If you add your Github username to your BiocCredentials account, it will import
the SSH keys you add on your Github account.
Best,
Nitesh
> On Mar 31, 2020, at 11:46 PM, Saskia Freytag wrote:
>
> Hi,
>
> I have added an SSH key to my GitHub and to the Biocredentials app, but I
> still cannot see my GitHub username appear. I think that my GitHub Username
> is also registered to another email and package (schex), could this lead to
> problems?
>
> Cheers,
>
> Saskia
> ___
>
> The information in this email is confidential and =\ i...{{dropped:17}}
___
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Re: [Bioc-devel] How can I maintain a stable list of source urls
Hi, this sounds very much like the bioconda approach, they have self-archived / mirrored the packages, which is not ideal. The Bio.tools people also ran into that issue earlier, and as mentioned in [1] is now fixed on the bioconductor side with stable download links. Yours, Steffen [1] https://github.com/bio-tools/biotoolsRegistry/issues/425#issuecomment-557270484 On Tue, 2020-03-31 at 12:27 -0700, Tim Sears wrote: > Hi > I am working to make bioconductor packages available through the nix > package manager (https://nixos.org/). Currently nixpkgs points to a > source > url on one of the bioconductor mirrors. nixpkgs tracks the url and a > sha256 > hash of the unpacked source link. Unfortunately the links themselves > often > disappear as the packages get updated either due to a version number > change > or changes inside the repo that affect the hash output. This breaks > corresponding nix package. This happens even for stable bioconductor > versions like 3.10. nixpkgs aims for reproducible builds, which means > when > things change, the url should reflect the change too and the contents > behich old urls should be preserved long enough to manage > the change. Do > you have any suggestions short of rebuilding a bioconductor mirror > with > immutable urls? > > Thanks, > TIm > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Current bits of interest: * PSI Spring Meeting Online, 23.-25.03.2020, http://www.psidev.info/hupo-psi-meeting-2020 * Annual symposium of German Society for Metabolomics e.V. (DGMet) in Berlin 4.-5th November. https://www.mdc-berlin.de/dgmet-2020 --- IPB HalleBioinformatics and Scientific Data Dr. Steffen Neumann http://www.IPB-Halle.DE *** Working from Home, available by Mail, Phone, Video Calls *** Weinberg 3 Tel. +49 (0) 345 5582 - 1470 06120 Halle +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] connectivity to hubs
There has been an issue reported that there is some connectivity / timeout issues happening to experimenthub and annotationhub. It seems to be intermittent but we are aware and investigating the issue. Thank you Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 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
