Re: [Bioc-devel] CNORfeeder building error
When I look at the git.bioconductor.org checkout of your package, There are no R functions and no man functions for those exports. Your commit on Mar 30 only updated the NAMESPACE and vignette. base) lori@lori-HP-ZBook-15-G2:~/b/Rpacks/CNORfeeder(master)$ grep -r "buildFeederObjectDynamic" * NAMESPACE:"buildFeederObjectDynamic", vignettes/CNORfeeder-vignette.Rnw:feederObject = buildFeederObjectDynamic(model = model, cnolist = cnolist, Please check your commits. You may have forgotten to git add the relevant files. Lori Shepherd 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 Enio Gjerga Sent: Thursday, April 2, 2020 3:54 PM To: Herv� Pag�s Subject: [Bioc-devel] CNORfeeder building error Hello, I am the maintainer of the CNORfeeder package. When I updated the package I added a few other functions. However, from the building I get the following error: package ornamespace load failed for �CNORfeeder� in namespaceExport(ns, exports): undefinedexports: *the names of the new functions I have added* I have added these function names on the NAMESPACE as exports and also they are in the /man function documentation (as .Rd files) and of course as R functions in /R. Please, what might be the reason for this? Should these new functions also be declared somewhere else which I am missing? I have run the 'R CMD INSTALL CNORfeeder' command in my terminal and the package seem to be built just fine. I am using Mac OS X El Captain. Best, Enio -- Enio GJERGA PhD student JRC-COMBINE RWTH Aachen Tel : +4917685132057 [[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. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] CNORfeeder building error
Hello, I am the maintainer of the CNORfeeder package. When I updated the package I added a few other functions. However, from the building I get the following error: package ornamespace load failed for ‘CNORfeeder’ in namespaceExport(ns, exports): undefinedexports: *the names of the new functions I have added* I have added these function names on the NAMESPACE as exports and also they are in the /man function documentation (as .Rd files) and of course as R functions in /R. Please, what might be the reason for this? Should these new functions also be declared somewhere else which I am missing? I have run the 'R CMD INSTALL CNORfeeder' command in my terminal and the package seem to be built just fine. I am using Mac OS X El Captain. Best, Enio -- Enio GJERGA PhD student JRC-COMBINE RWTH Aachen Tel : +4917685132057 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Development branch build error from celda
I think this is an intermittent connectivity issue and is safe to ignore. While today's build report has not yet officially posted, I check the report for you package and it seems to be all OK. Thank you for your diligence on investigating package ERRORs. Cheers, Lori Shepherd 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 Wang, Zhe Sent: Thursday, April 2, 2020 1:46 AM To: Bioc-devel@r-project.org Subject: [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 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] Help with tokay2 errors
On quick glance into the logs on tokay2 it looks like it may be an issue with MotifDb and not your package. In merge_motif it doesn't get to evaluating the code as it is hung up on trying to load the MotifDb library. Once this library is called, There are numerous: *** recursive gc invocation and somewhere in the middle of all these repeated lines is Error: package or namespace load failed for 'MotifDb': .onLoad failed in loadNamespace() for 'MotifDb', details: call: base::colSums(x, na.rm = na.rm, dims = dims, ...) error: bad binding access Execution halted Lori Shepherd 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 Benjamin Jean-Marie Tremblay Sent: Saturday, March 28, 2020 4:22 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Help with tokay2 errors Hi, Recently I've been having several examples fail on the tokay2 test machine, specifically the i386 examples. Unfortunately I don't have access to a windows machine to diagnose these failures right now, and the output that I can see shows no errors; the examples just end abruptly. I don't see these failures on my own computer (regular macOS, also docker bioc-devel image), so I�m at a bit of a loss as to how to go about fixing these. http://bioconductor.org/checkResults/devel/bioc-LATEST/universalmotif/tokay2-checksrc.html Any help would be greatly appreciated. Thanks, Benjamin Tremblay ___ 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] Final List of Deprecated Packages for Bioc3.11
Software package: DChIPRep and Workflow package: maEndToEnd User requested deprecation. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Shepherd, Lori Sent: Monday, March 30, 2020 11:36 AM To: bioc-devel@r-project.org Subject: Final List of Deprecated Packages for Bioc3.11 The Bioconductor Team is continuing to identify packages that will be deprecated in the next release to allow for the Bioconductor community to respond accordingly. The list will be updated monthly. This is the current list of deprecated packages for Bioc 3.11 : Maintainer requested deprecation: Software: QUALIFIER motifRG triform CVE proteoQC affypdnn splicegear Genominator IdMappingAnalysis IdMappingRetrieval manta RefNet AnalysisPageServer scfind kimod plw cn.mops cobindR LMGene sRAP gCMAP gCMAPWeb DESeq Annotation: org.At.tair.db hom.At.inp.db hom.Ce.inp.db hom.Dm.inp.db hom.Dr.inp.db hom.Hs.inp.db hom.Mm.inp.db hom.Rn.inp.db hom.Sc.inp.db KEGG.db (use KEGGREST instead) Unresponsive/not-maintained packages: Software: SELEX CTDquerier MTseeker readat anamiR MEAL BiSeq CALIB cellGrowth chroGPS DEDS LVSmiRNA MANOR MCRestimate nem PAPi pcaGoPromoter pint RIPSeeker SANTA waveTiling BayesPeak bgafun lol M3D MergeMaid IPPD biosvd birta DupChecker FEM geecc MaxContrastProjection mitoODE MoPS PowerExplorer Vega ExpermentData: MTseekerData RIPSeekerData The follow Annotation packages were deprecated in 3.10 and removed from 3.11 but not previously announced. MafDb.ESP6500SI.V2.SSA137.hs37d5 MafDb.EXP6500SI.V2.SSA137.GRCh38 It should be noted, we did try to reach out to these package maintainers multiple times and they were either unresponsive or had emails bounce. We encourage anyone that is familiar with a package maintainer on this list to reach out to them and notify them directly. Packages can be un-deprecated if a maintainer fixes the package to build/check cleanly before the next release and requests un-deprecation on the bioc-devel@r-project.org mailing list. We will be sending emails out to packages that have been broken across all platforms for an extended period of time as those are packages that are up for immediate deprecation if not corrected in a timely fashion. We will still be keeping track of failing packages and compiling a list to deprecate immediately after the release. This could have been because the package has reverse dependencies or was identified to late to deprecate in 3.11. We encourage anyone that knows the maintainers of these packages to reach out to them to fix their package to avoid deprecation. The current list for immediate deprecation in 3.12 is: DESeq MotIV NOISeq omicade4 PGSEA Starr VanillaICE 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
Re: [Bioc-devel] Unable to update maintainer email address
Hi, I've updated your email address to the one you are emailing from now. pierre.neuv...@math.cnrs.fr. Please "activate" you BiocCredentials account first and add SSH keys. Once you do that you'll be able to change the email on the description file. https://git.bioconductor.org/BiocCredentials/account_activation/ Best, Nitesh > On Apr 2, 2020, at 7:22 AM, Pierre Neuvial > wrote: > > Hello, > > I am the maintainer of the MANOR package. This package is listed in > "Unresponsive/not-maintained packages:" because I did not update my email > after moving to my current position, and this email does not exist anymore. > > I understand that I need to update the email in the DESCRIPTION of the > MANOR package with the one I am writing with. However, I don't think I can > do this because I do not have an active BiocCrendentials account yet, > and... I can't activate my BiocCredentials account, since the email > associated with the package is not working anymore. > > If this is the correct way to go, can a BioC admin update my email in the > DESCRIPTION of the MANOR package with the one I am writing with in order to > break this circle? > > All the best, > > Pierre > > [[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] Problems with Biocredentials
Yes, that is the problem. I'm not sure how you have two accounts for two
packages. It might be because you submitted both packages with different email
addresses as maintainer, one from a "Perkins" account and the other from "wehi"
account.
I've fixed the issue. Please try again, and see that you have access to all
your packages.
Best,
Nitesh
> On Apr 1, 2020, at 9:04 AM, Turaga, Nitesh
> wrote:
>
> 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}}
>
> ___
> 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
[Bioc-devel] Unable to update maintainer email address
Hello, I am the maintainer of the MANOR package. This package is listed in "Unresponsive/not-maintained packages:" because I did not update my email after moving to my current position, and this email does not exist anymore. I understand that I need to update the email in the DESCRIPTION of the MANOR package with the one I am writing with. However, I don't think I can do this because I do not have an active BiocCrendentials account yet, and... I can't activate my BiocCredentials account, since the email associated with the package is not working anymore. If this is the correct way to go, can a BioC admin update my email in the DESCRIPTION of the MANOR package with the one I am writing with in order to break this circle? All the best, Pierre [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
