Re: [Bioc-devel] Old package versions / Bioc archive of package's *.tar.gz releases?

On Thu, Oct 5, 2017 at 10:03 PM, Gabe Becker wrote: > Oh, and the svn/git walking knows about release branches so it will find > hot-patch versions correctly, as well. > In the Bioc case, I mean, not generally. And with that flurry of emails I'm off to bed. Best, ~G > > ~G

Re: [Bioc-devel] Old package versions / Bioc archive of package's *.tar.gz releases?

Oh, and the svn/git walking knows about release branches so it will find hot-patch versions correctly, as well. ~G On Thu, Oct 5, 2017 at 10:01 PM, Gabe Becker wrote: > Correct. The actual order of checks is: > >1. did switchr already retrieve that exact version for

Re: [Bioc-devel] Old package versions / Bioc archive of package's *.tar.gz releases?

Correct. The actual order of checks is: 1. did switchr already retrieve that exact version for something else and keep it around, 2. A GRANRepository object if one is specified (don't worry much about this one) 3. the manifest itself (cran and bioc source types are ignored, but it

Re: [Bioc-devel] Old package versions / Bioc archive of package's *.tar.gz releases?

That's really nice; I didn't know it could do all that. For my clarification, when using PkgManifest(..., type = "bioc") it'll search (i) the CRAN archives, (ii) the Bioconductor repos(es), and then (iii) the Bioconductor Git repos - is that a correct observation? (I installed from

Re: [Bioc-devel] Problem with html vignette in BiocStyle 2.5.39

?Hi Andrzej, thanks to your help everything is working fine now. Thanks a lot. Cheers, Stefan From: Andrzej Ole� Sent: Thursday, October 5, 2017 6:23 PM To: Stefan Mutter Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel]

Re: [Bioc-devel] Old package versions / Bioc archive of package's *.tar.gz releases?

In point of fact, it looks like IRanges 2.6.0 is an instance of that weakness, so was probably a bad example. 2.6.1 installs correctly, or would in it's native R/base bioc environment... (it fails for me in the library I have...) Also, the version on CRAN uses the bioc SVN, so may not work for

Re: [Bioc-devel] Old package versions / Bioc archive of package's *.tar.gz releases?

Henrik et al., My switchr package (on CRAN, github at: http://github.com/gmbecker/switchr, preprint of the paper here: https://arxiv.org/abs/1501.02284 ) can do this. In fact, installing (cohorts of) old versions of packages is one of it's primary purposes.

Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow

Thanks Val, and no worries. I'm looking forward to seeing some updated guidelines for the workflows, incorporating what we've discussed on the mailing list; if I know what to do, I'm happy to put in the effort on my end. -Aaron From: Obenchain, Valerie

Re: [Bioc-devel] Old package versions / Bioc archive of package's *.tar.gz releases?

On 10/05/2017 05:14 PM, Henrik Bengtsson wrote: On Thu, Oct 5, 2017 at 1:46 PM, Martin Morgan wrote: On 10/05/2017 01:50 PM, Henrik Bengtsson wrote: Is there an easily accessible archive for Bioconductor packages similar to what is provided on CRAN where you

Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow

About the DLL limit: Just wanna make sure you're aware of "new" environment variable R_MAX_NUM_DLLS available in R (>= 3.4.0). It allows you to push the current default limit of 100 open DLLs a bit higher. It can be set in .Renviron or before, e.g. $ R_MAX_NUM_DLLS=500 R This, of course,

Re: [Bioc-devel] Old package versions / Bioc archive of package's *.tar.gz releases?

On 10/05/2017 01:50 PM, Henrik Bengtsson wrote: Is there an easily accessible archive for Bioconductor packages similar to what is provided on CRAN where you can find all released versions of a package, e.g. https://cran.r-project.org/src/contrib/Archive/PSCBS/? Say I want to access the source

Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow

Glad this sparked some interesting dialogue! Regardless of what's decided, this change should have been announced on the list before implementing it. Sorry for changing the package out from under you. I recognize these workflows are the author's unique work and style will vary with personal

Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow

Just had a look at the use of Makefiles in vignettes/; it seems like the Makefile controls the conversion to PDF after Sweave'ing. So it probably can't be used to control the order of Sweaving, though there doesn't seem to be any mention of how the order is controlled. If it's alphanumeric, we

Re: [Bioc-devel] BioC 3.6: BUILD/CHECK reports are not updating.

Hi It can take up to 24 hours to see the changes pushed to the Bioconductor server and be reflected on the build report. There is normally a new build report generated daily. There was an issue on our end that prevent the build report from completing yesterday but there should be a new

Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow

Breaking up long workflows into several smaller "modules" each with a clearly defined input and output is a good idea, certainly for didactic & maintenance reasons. It doesn't "solve" the DLL issue though, it only avoids it (for now)... I believe you can use a Makefile for your vignettes

Re: [Bioc-devel] Organism.dplyr::supportedFilters warning

We've updated GSEABase on devel yesterday so that it should build correctly. This will fix the warning that was being sent off by EnrichmentBrowser. The changes may take a few days to propagate. From: Bioc-devel on behalf of

Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow

This may relate to what I was thinking with respect to solving the DLL problem, by breaking up large workflows into modules that can be executed in separate R sessions. The same approach would also make it easier to associate package dependencies with specific parts of the workflow. In my

[Bioc-devel] Old package versions / Bioc archive of package's *.tar.gz releases?

Is there an easily accessible archive for Bioconductor packages similar to what is provided on CRAN where you can find all released versions of a package, e.g. https://cran.r-project.org/src/contrib/Archive/PSCBS/? Say I want to access the source code for affy 1.18.0. Here are the two approaches

Re: [Bioc-devel] Duplicate commit error on and off

Done. If you clone from Bioconductor again, you should get a clean copy just as after the transition. If you have questions let me know. Best, Nitesh > On Oct 5, 2017, at 1:05 PM, Thomas Girke wrote: > > Yes, let's just do it this way. > > Thomas > > On Thu, Oct

Re: [Bioc-devel] Duplicate commit error on and off

Yes, let's just do it this way. Thomas On Thu, Oct 5, 2017 at 9:36 AM Turaga, Nitesh wrote: > It would be easier. I can do it and it would take you back to, > > commit c84c7b5fbdf1419af5030b66f8a759d29307f40b (git-svn) > Author: Herve Pages >

Re: [Bioc-devel] BioC 3.6: CHECK report

The development branch of bioconductor is a place for developers and maintainers of packages to implement changes or new features. Some of these changes could effect the expected output or behavior of functions, it is therefore possible to get new ERRORs if a package your package depends on

Re: [Bioc-devel] Duplicate commit error on and off

It would be easier. I can do it and it would take you back to, commit c84c7b5fbdf1419af5030b66f8a759d29307f40b (git-svn) Author: Herve Pages Date: Mon Apr 24 19:50:57 2017 + bump x.y.z versions to odd y after creation of 3_5 branch git-svn-id:

Re: [Bioc-devel] Difficulty obtaining access to BioC git repository

No problem. As a heads up for the future, the mailing list might get a quicker response vs the support site as far as GIT goes. Best, Nitesh > On Oct 5, 2017, at 12:12 PM, Raborn, R. Taylor wrote: > > Hi Nitesh; > > I see- this makes sense. I apologize for my error

[Bioc-devel] BioC 3.6: CHECK report

Hi. I recently received an e-mail about a check error in the RUnit test in my package "coexnet". https://bioconductor.org/checkResults/3.6/bioc-LATEST/coexnet/malbec1-checksrc.html I want to ask if my package was already in Bioconductor repository as "development version", Why do I have this

Re: [Bioc-devel] Difficulty obtaining access to BioC git repository

Hi Nitesh; I see- this makes sense. I apologize for my error and appreciate you providing me with access. Thank you for your assistance with this. Best regards, Taylor > On Oct 5, 2017, at 12:04 PM, Turaga, Nitesh > wrote: > > Hi, > > You have submitted

Re: [Bioc-devel] Difficulty obtaining access to BioC git repository

Hi, You have submitted multiple times with bad ID’s. This has not gone too well with our application and fails add your key. You first submitted “rtraborn” with a set of keys, and then with the same set of keys with you valid SVN ID. The system does not add the same key twice with two separate

[Bioc-devel] Difficulty obtaining access to BioC git repository

Hello: I’m a co-developer and package maintainer for TSRchitect, a relatively new Bioconductor package. We wish to push package updates to the Bioconductor git repo, but as of yet I have been unable to do so. This post

[Bioc-devel] BioC 3.6: BUILD/CHECK reports are not updating.

Hi, I have recently (Tue 03) made some changes for my package (MIGSA). However I cant see if the code is really being modified at BioConductor's package manager (github). So I wanted to check if at least the check reports are being updated, however, it seems that this is not being done daily. At

[Bioc-devel] Fwd: Duplicate commit error on and off

Begin forwarded message: From: ni41435_ca > Subject: Re: [Bioc-devel] Duplicate commit error on and off Date: October 5, 2017 at 6:56:51 AM EDT To: Thomas Girke > Hi Thomas,

Re: [Bioc-devel] new package submission (pcxn) Abnormal build result

Yes, this seems to be a problem on our side. We are looking into it. For now you can ignore this ERROR. There was a similar post here: https://stat.ethz.ch/pipermail/bioc-devel/2017-September/011773.html Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of

Re: [Bioc-devel] Problem with html vignette in BiocStyle 2.5.39

Hi Andrzej, Thanks for your quick reply. It's very well possible I forgot to attach the file. Sorry for that. I will double check but I also realised that I have included the figure into markdown with a different and most likely incorrect syntax. I will try your way and if the problem

Re: [Bioc-devel] Problem with html vignette in BiocStyle 2.5.39

Dear Stefan, Thanks for your feedback. I didn't find the R Markdown sample document you mentioned, maybe you forgot to attach it. The following minimal example illustrates how to include figures from external files such that they are numbered and contain captions. Best, Andrzej --- output:

Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow

I agree it is nice to be able to only load the packages needed for a certain section of a vignette and not the whole thing. And that too many `::` can make code look unwieldy (though some may actually increase readability). But relying on manually sprinkled in `library` calls seems like a

Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow

On 5 October 2017 00:11, Aaron Lun wrote: > Here's another two cents from me: > > The explicit library() calls allow for easy copy-pasting if people > only want to use/adapt a section of the workflow. In such cases, > calling "library(simpleSingleCell)" could drag in a lot of unnecessary >