Re: [Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble

Thanks everyone for playing along! The order of packages doesn't influence order of installation, otherwise the user would have to know the dependency graph (although I think we're starting to become intimately familiar with such graphs!) Like Felix I'm also of the opinion that the source and b

Re: [Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble

Hi, Thanks for the discussion and the insight into possible solutions. I currently have the same problem with settings up an RNAmodR GitHub Action. This fails because the RNAmodR requires RNAmodR.Data, which suggests GenomicRanges, which then leads to GenomeInfoDb and GenomeInfoDbData. What st

[Bioc-devel] Bioconductor git repository commits have resumed

Dear Maintainers, The commits to the Bioconductor repository have been resumed. The new branch RELEASE_3_11 has been created for all packages. All maintainers should have access to the "master" (devel branch) and the RELEASE_3_11 branch of their packages. Best regards, Nitesh Turaga _

[Bioc-devel] All commits to Bioconductor git repository frozen

Dear Maintainers, As per my email about an hour ago, I've frozen the commits to Bioconductor git repository at 1:30pm EDT. Once we create the release 3.11 branch, I will re-enable access. The process will take about 2.5 - 3 hours. Best, Nitesh __

[Bioc-devel] Fwd: Creating Bioconductor 3.11 branch on April 27th - 1:30PM EDT

Dear Maintainers, Please keep in mind that we are on schedule for our release as given in http://bioconductor.org/developers/release-schedule/ . Today (April 27th 2020) at 1:30pm EDT, I will freeze the commits to Bioconductor until further no

Re: [Bioc-devel] regutools: request to add more git push access

Hi Nitesh! Yes, this it's the email address I will be using ( car.bar...@gmail.com). Thank you Carmina El lun., 27 abr. 2020 a las 5:59, Nitesh Turaga () escribió: > Hi Leo, > > I've added you and Alejandro to the regutools package. > > Carmina and Emiliano, please confirm the email addresses you

[Bioc-devel] Creating Bioconductor 3.11 branch on April 27th - 1:30PM EDT

Dear Maintainers, Please keep in mind that we are on schedule for our release as given inhttp://bioconductor.org/developers/release-schedule/. Today (April 27th 2020) at 1:30pm EDT, I willfreezethecommitsto Bioconductor until further notice so we can create the RELEASE_3_11 branch for all pa

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

Hi, I am not sure if I am going to have to wait to submit extra revisions. However, I am unfortunately having the same issue (even though I tested using the temporary directory instead of the current working directory, in COHCAP (v.1.33.4). I also tested changing the file path to the temporar

Re: [Bioc-devel] regutools: request to add more git push access

Thank you Nitesh =) And hm... I missed a couple of words in my email subject. Oops :P On Mon, Apr 27, 2020 at 11:18 AM Carmina Barjon wrote: > > Hi Nitesh! Yes, this it's the email address I will be using > (car.bar...@gmail.com). > Thank you > Carmina > > El lun., 27 abr. 2020 a las 5:59, Nite

Re: [Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble

Hi, I also ran more tests, which makes me think that the issue was with the list of dependencies we were asking `remotes` to install. First, regarding the second to last email from Charlotte, the step-wise installation I did mostly using remotes was not ideal. I found a complicated scenario in a

Re: [Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble

Hi again, as for getting the immediate dependencies, this is what remotes does internally (it includes also recommended packages though): deps <- remotes::local_package_deps(pkgdir = ".", dependencies = TRUE) > I guess I would further simplify the problem by eliminating from 'deps' the > packa

Re: [Bioc-devel] No build report

It looks like you had merge conflicts with the version bump to 1.1.1 until late Sat night: commit 199ad444e10c81c472deefe5dff5e32dff977b41 Author: Quy Xuan Cao Date: Sat Apr 25 23:33:03 2020 -0400 Bump up to version 1.1.1 on github This would be too late to be picked up on Sunday's bui

[Bioc-devel] No build report

Dear all, I have pushed my updated package PERFect to Bioconductor last weekend but I haven't seen any build report yet. Is there something I can do in this situation? Thanks, Quy -Original Message- From: Bioc-devel On Behalf Of Nitesh Turaga Sent: Monday, April 27, 2020 9:00 AM To:

Re: [Bioc-devel] regutools: request to add more git push access

Hi Leo, I've added you and Alejandro to the regutools package. Carmina and Emiliano, please confirm the email addresses you'll be using. I can add you both as well, and create BiocCredentials accounts for you. Nitesh On 4/26/2020 11:42 PM, Leonardo Collado Torres wrote: Hi Nitesh, Could

Re: [Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble

Personally, I wouldn't trust remotes to get the Bioconductor repositories, and hence the dependency graph, correct. I say this mostly because of problems to get BiocManager to get the repositories right during each phase of the Biocoonductor release cycle, not to diss the remotes package. I'd g

Re: [Bioc-devel] Question about "Warning: '.local' is deprecated."

Thank you! Found it: "flowCore::description" is old, "flowCore::keyword" is replacement. Best regards Jakob From: Martin Morgan Sent: 27 April 2020 10:28 To: Jakob Theorell ; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Question about "Warning: '.local' is

Re: [Bioc-devel] Question about "Warning: '.local' is deprecated."

I would suggest forcing warnings to errors options(warn=2) and then when the now-error occurs using traceback() to see what is wrong -- I think this is a call to a deprecated S4 method, and what you'd really like is the method signature. Martin On 4/27/20, 2:58 AM, "Bioc-devel on be

Re: [Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble

Thanks both, this is very informative! It seems to me (at least from my small example) that what causes the actual installation failure is not the “binary-before-source” installation (as Martin said, this would not fail since the binaries are not loaded), but that the source packages are instal