Re: [Bioc-devel] Update CARNIVAL maintainer

Hi Enio and Olgo, I’ve taken care of this. Olga, you should have access to the package as soon as you add your SSH keys to your git.bioconductor.org/BiocCredentials account. You’ll get a private email from me about your account information.

Re: [Bioc-devel] Co-maintainer for SpectralTAD and TADCompare

Hi Mikhail, You should have access to your packages now. Best, Nitesh > On Oct 19, 2020, at 3:13 PM, Mikhail Dozmorov > wrote: > > Hello, > Would it be possible to add me as a co-maintainer to two packages? > https://bioconductor.org/packages/SpectralTAD/ >

Re: [Bioc-devel] R 4.0.3 for Windows R CMD check finds 'abort'

Sorry, there was mistype in previous email. Here is the reproducible example again. This code produces the NOTE when run in a fresh R 4.0.3 for Windows session: library(Rcpp) Rcpp.package.skeleton("TestPack", example_code = TRUE) library(devtools) check("TestPack") > -Original

Re: [Bioc-devel] R 4.0.3 for Windows R CMD check finds 'abort'

Hi Martin and Vince, Thanks for the responses. I noticed first noticed this issue (false positive R CMD NOTE about abort) when it appeared with R-devel for Windows a few months ago. The same behaviour has now appeared in R 4.0.3. It is specific to Windows, R 4.0.3 or higher and Rtools40. It

Re: [Bioc-devel] R 4.0.3 for Windows R CMD check finds 'abort'

On Mon, Oct 19, 2020 at 1:41 PM Martin Morgan wrote: > Just to respond that I don't have a clear answer for you; I would guess > that there is a change upstream of your package, and that the NOTE is > spurious. If this also occurs on a non-Bioconductor Windows machine then it > would be

[Bioc-devel] Co-maintainer for SpectralTAD and TADCompare

Hello, Would it be possible to add me as a co-maintainer to two packages? https://bioconductor.org/packages/SpectralTAD/ https://bioconductor.org/packages/TADCompare/ It'll be best if both Kellen, the current maintainer, and I will have push access. Thanks, Mikhail [[alternative HTML

Re: [Bioc-devel] R 4.0.3 for Windows R CMD check finds 'abort'

Just to respond that I don't have a clear answer for you; I would guess that there is a change upstream of your package, and that the NOTE is spurious. If this also occurs on a non-Bioconductor Windows machine then it would be appropriate to bring this up on another forum, R-devel or

Re: [Bioc-devel] Orchid ID invalid according to BiocCheck

Thanks! This will also help me ^^ https://orcid.org/-0003-2140-308X Best, Leo Leonardo Collado Torres, Ph. D. Investigator LIEBER INSTITUTE for BRAIN DEVELOPMENT 855 N. Wolfe St., Suite 300 Baltimore, MD 21205 lcolladotor.github.io lcollado...@gmail.com On Mon, Oct 19, 2020 at 7:43 AM

Re: [Bioc-devel] Bioconductor 3.12 db0s, OrgDbs and TxDbs now available

My apologies - I seem to have a typo in the names of the updated OrgDb packages. Please see the following corrected list: org.Ag.eg.db_3.12.0.tar.gz org.At.tair.db_3.12.0.tar.gz org.Bt.eg.db_3.12.0.tar.gz org.Ce.eg.db_3.12.0.tar.gz org.Cf.eg.db_3.12.0.tar.gz

Re: [Bioc-devel] [EXTERNAL]Re: A question about r package update

The latest version is now reflected in the build report and on the package landing page. Please again review timings on this page that the landing pages are only updated after a successful build with version bump hence why the full update on the build report and landing pages can take up to 48

Re: [Bioc-devel] VERSO issue #1689

We are sorry for the delay. We try to get to package reviews within 2 weeks of submission. Package reviews are only part of the core team task and as you can imagine release time is busy. Nitesh will have a review for you shortly. Lori Shepherd Bioconductor Core Team Roswell Park

Re: [Bioc-devel] Orchid ID invalid according to BiocCheck

Yes, I’ll create a PR. From: Vincent Carey Date: Monday, 19 October 2020 at 12:36 To: "Manders-2, F.M." , bioc-devel Subject: Fwd: [Bioc-devel] Orchid ID invalid according to BiocCheck forwarding to bioc-devel -- Forwarded message - From: Vincent Carey

Re: [Bioc-devel] Orchid ID invalid according to BiocCheck

Well I learnt something new today! "The final character, which may also be a letter "X" representing the value "10" [..], is a MOD 11-2 check digit conforming to the ISO/IEC 7064:2003 standard." -

Re: [Bioc-devel] Orchid ID invalid according to BiocCheck

It seems to be a valid ID: https://support.orcid.org/hc/en-us/articles/360053289173-Why-does-my-ORCID-iD-have-an-X- Maybe BiocCheck doesn’t realize the ID can end with an X? From: Vincent Carey Date: Monday, 19 October 2020 at 12:20 To: "Manders-2, F.M." Cc: Alessandro Lussana via Bioc-devel

[Bioc-devel] Fwd: Orchid ID invalid according to BiocCheck

forwarding to bioc-devel -- Forwarded message - From: Vincent Carey Date: Mon, Oct 19, 2020 at 6:33 AM Subject: Re: [Bioc-devel] Orchid ID invalid according to BiocCheck To: Manders-2, F.M. Cc: Alessandro Lussana via Bioc-devel looks like BiocCheck/checks.R:

Re: [Bioc-devel] Orchid ID invalid according to BiocCheck

looks like BiocCheck/checks.R:validID <- grepl("[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{4}", orcid) has to change -- do you have time to determine the correct regex for this and file a PR? On Mon, Oct 19, 2020 at 6:31 AM Manders-2, F.M. < f.m.mand...@prinsesmaximacentrum.nl> wrote: >

Re: [Bioc-devel] Orchid ID invalid according to BiocCheck

Yes, the X is correct (https://orcid.org/-0001-6197-347X). I don’t know why I have an X there and not a number. From: Vincent Carey Date: Monday, 19 October 2020 at 12:20 To: "Manders-2, F.M." Cc: Alessandro Lussana via Bioc-devel Subject: Re: [Bioc-devel] Orchid ID invalid according to

Re: [Bioc-devel] Orchid ID invalid according to BiocCheck

person("Freek", "Manders", email = "f.m.mand...@prinsesmaximacentrum.nl", role = c("aut"), comment = c(ORCID = "-0001-6197-347X")), is what I see in a current checkout. is "X" at the end correct? maybe there is an encoding issue? On Mon, Oct 19, 2020 at 6:14 AM Manders-2, F.M. <

[Bioc-devel] Orchid ID invalid according to BiocCheck

Hi all, BiocCheck is giving me a note that my ORCID ID is invalid ("Invalid ORCID ID for Freek Manders"). However, I see nothing wrong with the ID. It also seems to work well on the dev page of my package (MutationalPatterns) Clicking on the green ID circle, sends me to my page just fine. Is

Re: [Bioc-devel] VERSO issue #1689

I can't speak for the reviewer, but the package currently has 2 WARNINGS. If I were you, I would fix those warnings and push the fixes to Github, at which point the package will be re-built and re-checked. You're not supposed to have any ERRORS / WARNINGS when you submit. I would also look at the

[Bioc-devel] VERSO issue #1689

Dear Bioconductor Staff, We have submitted a new package VERSO, by opening a new issue ( https://github.com/Bioconductor/Contributions/issues/1689) and a moderator (CCed) was assigned 17 days ago. Since that, we did not receive any feedback. As the submission deadline is approaching we are