[Bioc-devel] Data hosting for workflow packages

Hi all, We are thinking of developing a workflow package which requires large input files. It says here that data for workflow packages should ideally be from other data packages or on the web. Is it alright to host the data on Zenodo and

Re: [Bioc-devel] Ask for help to debug the error on riesling1

Hi Martin, Thank you for going so deep. I tried R -d "valgrind --leak-check=full --track-origins=yes" -f plotInteractionData.R to locate the exact line where initialed the possible leak. Is there any other possibility that killed the process and did not leave any error log information?

Re: [Bioc-devel] Suppressing messages from Rprofile

Correcting: the env var is R_LIBS_USER and nothing else. /Henrik On Wed, Apr 7, 2021 at 1:20 PM Henrik Bengtsson wrote: > > Can you go via a temporary file instead, i.e. output what you want to > grab to a temporary file and pull the info from that instead? > > Side tracking ... > > > I thought

Re: [Bioc-devel] Suppressing messages from Rprofile

Can you go via a temporary file instead, i.e. output what you want to grab to a temporary file and pull the info from that instead? Side tracking ... > I thought about using --vanilla but I use .Rprofile to set my library path, > so ignoring that file completely defeats the point in my setup.

Re: [Bioc-devel] Updates to BiocFileCache, AnnotationHub, and ExperimentHub

FWIW, I ran into a similar problem when I moved R.cache (https://cran.r-project.org/package=R.cache) from using ~/.Rcache to ~/.cache/R/R.cache (etc). I decided on making it 100%-backward compatible, i.e. if there's already a legacy ~/.Rcache cache folder, it'll keep using that, otherwise the new

Re: [Bioc-devel] BFG repo cleanup for package under review

Hi Spencer, I�ve fixed the issue please try now. Best, Nitesh From: Nitesh Turaga Date: Wednesday, April 7, 2021 at 1:31 PM To: Spencer Nystrom , bioc-devel@r-project.org Subject: Re: [Bioc-devel] BFG repo cleanup for package under review Hi Spencer, I�ll take a look at this today and get

Re: [Bioc-devel] Ask for help to debug the error on riesling1

I followed these steps, more or less, to configure and use valgrind on the Bioconductor docker image. https://gist.github.com/mtmorgan/77f9d92d81830eeb7f254809b445874d For this particular use I - added the valgrind system dependency - installed trackViewer and it's 'Suggests' dependencies in

Re: [Bioc-devel] BFG repo cleanup for package under review

Hi Spencer, I�ll take a look at this today and get back to you Thanks for the reminder. Best, Nitesh From: Bioc-devel on behalf of Spencer Nystrom Date: Wednesday, April 7, 2021 at 1:24 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] BFG repo cleanup for package under review Sorry

[Bioc-devel] BFG repo cleanup for package under review

Sorry to ping about this twice, but my guess is this got buried over the long weekend. I need some help getting a cleaned up repo force pushed to the bioconductor repository ( g...@git.bioconductor.org:packages/memes ). This is for a package under review here:

Re: [Bioc-devel] Updates to BiocFileCache, AnnotationHub, and ExperimentHub

> There is no guarantee we would be under the right user to have permissions to > move the cache automatically and would not want to leave it in a broken state. Well, can't you try? If people follow your 4.1 instructions and they don't have permissions, the cache will be broken anyway. But

Re: [Bioc-devel] Updates to BiocFileCache, AnnotationHub, and ExperimentHub

The experience: > ah = AnnotationHub() Error in AnnotationHub() : As of AnnotationHub (>2.23.2), default caching location has changed. Problematic cache: /home/stvjc/.cache/AnnotationHub To continue with default caching location, See AnnotationHub vignette TroubleshootingTheCache section

Re: [Bioc-devel] Updates to BiocFileCache, AnnotationHub, and ExperimentHub

For convenience here are relevant sections of the new vignette. Give it a try and let us know. This is "devel". 4Default Caching Location Update As of BiocFileCache version > 1.15.1, the default caching location has changed. The default cache is now controlled by the function

Re: [Bioc-devel] Updates to BiocFileCache, AnnotationHub, and ExperimentHub

There is no guarantee we would be under the right user to have permissions to move the cache automatically and would not want to leave it in a broken state. We could start a fresh cache in the new location but there would be no way to combined an old cache and a new cache and there would be no

Re: [Bioc-devel] Updates to BiocFileCache, AnnotationHub, and ExperimentHub

Woah, I missed the part where you said that there would be an error. This does not sound good. Users are going to flip out, especially when EHub and AHub are not visible dependencies (e.g., scRNAseq, celldex). It also sounds completely unnecessary for EHub and AHub given that the new cache can

[Bioc-devel] Suppressing messages from Rprofile

I have the following line in the configure.ac for rhdf5filters, which returns the location of the HDF5 headers distributed with Rhdf5lib: RHDF5_INCLUDE=`"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e 'cat(system.file("include", package="Rhdf5lib"))'` For me the output is a path like

Re: [Bioc-devel] Ask for help to debug the error on riesling1

Hi Herv�, Thank you for the information. I will try to figure out. Jianhong. From: Herv� Pag�s Sent: Wednesday, April 7, 2021 1:54 AM To: Jianhong Ou, Ph.D. ; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Ask for help to debug the error on riesling1 Hi

Re: [Bioc-devel] Updates to BiocFileCache, AnnotationHub, and ExperimentHub

Mostly to lighten the dependency tree using tools that is built in with R would remove one additional dependency. Also clarity; the tools directory adds an R folder for distinction that they are used with R packages which seemed like if a user was ever investigating, they would have a better

Re: [Bioc-devel] Updates to BiocFileCache, AnnotationHub, and ExperimentHub

rebook and basilisk are also currently using rappdirs. I would be interested in the motivation behind the switch for the Hubs and whether that is applicable to those two packages as well. -A On 4/5/21 6:41 AM, Kern, Lori wrote: We are in process of making some major updates to the caching in