Re: [Bioc-devel] Fwd: BioC 3.12 coming soon, package a4 and a4Base need your attention!

Dear bioc team, I am getting the following warning that I do not understand and cannot reproduce locally (and my search online didn't help): * checking whether package ‘artMS’ can be installed ... WARNING Found the following signific

Re: [Bioc-devel] Can we still patch a broken package in 3_11

Dear Lori, thank you for the info. I kind of expected it. The master branch is already updated. Best, Christian On Wed, 2020-10-21 at 11:49 +, Kern, Lori wrote: > The RELEASE_3_11 branch is frozen and will not be updated. Please > update in your current master branch so the changes will be

[Bioc-devel] Ris: Package update before october 23rd deadline and build errors [duplicated, wrong email address previous]

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Re: [Bioc-devel] merging DFrames

Thank you both - issue has just been opened. Merci Hervé for pointing out the direct use of the `List()` constructor. Laurent From: Michael Lawrence Sent: 21 October 2020 19:13 To: Pages, Herve Cc: Laurent Gatto; bioc-devel@r-project.org Subject: Re: [Bi

Re: [Bioc-devel] 3.12 builds

Please review this page on timing for build report and landing page updates. bioconductor.org/developers/how-to/troubleshoot-build-report/ The recent commit to 0.99.23 was only today. This would not have been in time for today's build report and should be reflected on tomorrow's build report.

Re: [Bioc-devel] 3.12 builds

Hi Herve, Can you clarify what you mean by after tomorrow? The deadline is Friday, October 23rd correct? Is there a time of day submissions need to be made by? Best, --- Christopher Eeles Software Developer BHK Laboratory Princess Margaret Cancer Centre University Health Network -Original

Re: [Bioc-devel] merging DFrames

Laurent, Thanks for bringing this up and offering to help. Yes, please raise an issue. There's an opportunity to implement faster matching than base::merge(), using stuff like matchIntegerQuads(), findMatches(), and grouping(). grouping() can be really fast for character vectors, since it takes a

Re: [Bioc-devel] 3.12 builds

Thank you, Herve, for the update. For the package msImpute, the latest commit shown on the recent build report points to v0.99.23, which is also the version on git (master devel), but this is not the version displayed on the build report, or the landing page. Do I need to take any actions? Muc

Re: [Bioc-devel] Package update before october 23rd deadline and build errors [duplicated, wrong email address previous]

Hi Giulia, Today's report is available. Unfortunately ISAnalytics tests are still failing on Windows: https://bioconductor.org/checkResults/devel/bioc-LATEST/ISAnalytics/tokay1-checksrc.html Note that you have this warning at the beginning of the tests: > test_check("ISAnalytics") Warn

Re: [Bioc-devel] Package update before october 23rd deadline and build errors [duplicated, wrong email address previous]

Hi Lori, thanks for your reply, unfortunately the problem persists, same as the previous build it appears to have issues with BiocParallel that we don't have both on local machines and github actions server machines. What should we do? Thank you Il 21/10/2020 14:33, Kern, Lori ha scritto: > We

[Bioc-devel] 3.12 builds

Hi developers, Sorry that we didn't have an updated report yesterday (Tuesday October 20) for the BioC 3.12 builds. The new report for today is out: https://bioconductor.org/checkResults/3.12/bioc-LATEST/ Please address any remaining issue with your packages as soon as possible. Only two da

Re: [Bioc-devel] merging DFrames

Hi Laurent, I think the current implementation was just an expedient to have something that works (in most cases). I don't know if a proper implementation that doesn't go thru data.frame is on the TODO list. Michael? I suggest you open an issue on GitHub under S4Vectors. Cheers, H. PS: Note t

[Bioc-devel] merging DFrames

When merging DFrame instances, the *List types are lost: The following two instances have NumericList columns (y and z) d1 <- DataFrame(x = letters[1:3], y = List(list(1, 1:2, 1:3))) d2 <- DataFrame(x = letters[1:3], z = List(list(1:3, 1:2, 1))) d1 ## DataFrame with 3 rows and 2 columns ##

[Bioc-devel] Windows build warnings from basilisk configure file

Hi, I have submitted the package dasper as an additional package to megadepth to Bioconductor 3.12: https://github.com/Bioconductor/Contributions/issues/1696 dasper interfaces into python using the Bioconductor package basilisk. I’ve included a configure file in the root of the dasper package f

Re: [Bioc-devel] Access denied to lpNet package

Hi Lars, I’ve resolved your issue. You should have access now. Best regards, Nitesh > On Oct 20, 2020, at 5:21 AM, Prof.Dr. Lars Kaderali > wrote: > > Dear Bioconductor team, > > I changed institution and my old email address @tu-dresden.de no longer > exists. The packages RNAither and RC

[Bioc-devel] Bioconductor Developers Forum - 22th October

Dear all, The next Developers Forum will take place this coming Thursday 22th Oct at 09:00 PDT / 12:00 EDT / 18:00 CEST - You can find a calendar invite at https://tinyurl.com/y4y2xptb We will be using BlueJeans and the meeting can be joined via: https://bluejeans.com/114067881 (Meeting ID: 114 0

[Bioc-devel] Package update before october 23rd deadline and build errors

Hello, bioconductor team, I'm one of the contributors for the package ISAnalytics. We pushed some changes we would like to be included in the release for bioconductor 3.12 a couple of days ago but the build report still refers to the older version, did we miss the deadline for updates or is it

Re: [Bioc-devel] Package update before october 23rd deadline and build errors [duplicated, wrong email address previous]

We are sorry for the inconvenience. There was an issue generating the build report, again. We hope to have it resolved and have the new build report posted later today. I do see the 0.99.13 updates in our git repository so they were pushed up and should be reflected in the next posted build r

Re: [Bioc-devel] Can we still patch a broken package in 3_11

The RELEASE_3_11 branch is frozen and will not be updated. Please update in your current master branch so the changes will be included in the upcoming release. thank you. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformat

Re: [Bioc-devel] MOFA package deprecation

Hi Lori, Thanks for taking care of this. MOFAdata is still in use, thanks for checking. Best Britta > On 21. Oct 2020, at 13:42, Kern, Lori wrote: > > Thank you for letting us know. Yes I can specialize the message to point > users to MOFA2. I will take care of this later today. > > Does

Re: [Bioc-devel] MOFA package deprecation

Thank you for letting us know. Yes I can specialize the message to point users to MOFA2. I will take care of this later today. Does MOFA2 still use the accompanied data package MOFAdata or should that also be deprecated? Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Canc

[Bioc-devel] MOFA package deprecation

Dear Bioconductor core team, I would like to deprecate the MOFA package as it has been superseded by MOFA2. Is it possible to add a note for users to turn to MOFA2 in the deprecation warning for MOFA? Best, Britta [[alternative HTML version deleted]]

[Bioc-devel] Package update before october 23rd deadline and build errors [duplicated, wrong email address previous]

Hello, bioconductor team, I'm one of the contributors for the package ISAnalytics. We pushed some changes we would like to be included in the release for bioconductor 3.12 a couple of days ago but the build report still refers to the older version, did we miss the deadline for updates or is it