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Is it permitted (tolerated? welcomed? discouraged?) to enhance and extend my package's vignette after the release? - Paul

How do I checkout the development version of my package? I imagine it is some variation on this, which gets the released version: svn co --username='??' --password='??' https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RCytoscape Thanks! - Paul

My package trena fails on all platforms with this error: there is no package called ?BSgenome.Athaliana.TAIR.TAIR9? Is Arabidopsis no longer supported by bioc? I remember some discussion related to this over the summer. - Paul

I am confused about the proper directory in which to put the vignette for a package ('RCytoscape') I am submitting. It appears that <packageName>/man is where the .Rd files go, one per method. Do I use man for the...

In a quick search of the R website just now, I found no mention of a unit testing framework for R. I hope to find something in the style of Java's JUnit, or Python's unittest. Is such a...

Are there any special techniques you can advise me of, for installing and running two concurrent R/bioc versions installed on Mac OS? I wish to have the latest build of the devel version without sacrificing the current release as...

Warning: replacing previous import ?RMySQL::dbApply? by ?RPostgreSQL::dbApply? when loading ?trena? We do not call dbApply directly anywhere in the package. I imagine it is called routinely by functions that we do call. Any suggestions on how to clear...

https://master.bioconductor.org/checkResults/3.9/bioc-LATEST/trena/malbec2-checksrc.html Warning in .seqlengths_TwoBitFile(x) : mustOpen: Can't open /home/biocbuild/bbs-3.9-bioc/R/library/BSgenome.Hsapiens.UCSC.hg38/extdata/single_sequences.2bit to read...

On Oct 11, 2012, at 11:25 AM, Steve Lianoglou wrote: > I'm +0 on not including default values, but whatever the decision is, > agree w/ you that getPromoterSeq() and promoters() should have the > same defaults (I actually never knew...

Is there some way -- perhaps an argument to biocLite -- for downloading and installing a package from the devel branch? I'm trying to find an easy way for a user to get RCytoscape 1.1.25, just built, from the...

Our package ?trena? has had build errors these last two weeks. I have not yet been able to reproduce them on a macOS laptop. Would it be sensible to get the latest release and devel docker images for Bioconductor? Are...

By example: https://github.com/Bioconductor/KEGGREST -> github project homepage displays https://github.com/Bioconductor/BrowserViz -> 404 Yet this works fine: git clone git at git.bioconductor.org:packages/BrowserViz.git Is visibility at github.com/Bioconductor therefore conditional? My...

Dear Bioc, I have added the lasted HOCOMOCO motifs to MotifDb but changed no code. The package 1.29.6 dumps core during in the bioc devel linux build, and fails perhaps similarly on windows. http://bioconductor.org/checkResults/devel...

In the RCytoscape package I have a convenience function which returns the values of a specified edge attribute, for all edges in the graph. It is ponderously slow on a graph of 9000 edges. I define it this way: function...

Warning in .seqlengths_TwoBitFile(x) : mustOpen: Can't open /home/biocbuild/bbs-3.9-bioc/R/library/BSgenome.Hsapiens.UCSC.hg38/extdata/single_sequences.2bit to read: No such file or directory Timing stopped at: 0.176 0 0.175...

Maybe this is already known. As recently as April 4th, a single-package build initiated from a git push trigger produced reports for all three architectures: merida2 (OS X), malbec2 (linux), and tokay2 (windows). Since then, and still today, I...

Any tips on how to generate html from man/*Rd files and the package vignette, so that I can assemble all that information into an external website? ... suitable for further development. My motivation: I'd like to provide and frequently...

On Sep 12, 2019, at 3:13 PM, Pages, Herve <hpages at fredhutch.org> wrote: > > AFAIK the build machines have web browsers. Hi Herve, I?d like to do my local linux testing of igvR using the same web browser...

Maybe this is already known. Maybe it?s my error. As recently as April 4th, a single-package build, initiated from a git push trigger, produced reports for all three architectures: merida2 (OS X), malbec2 (linux), and tokay2 (windows). Since...

Hi Seth, It looks like the gaggle package failes to check on OSX due to a build error on graph. I'll leave that one to you for now, if I may... As for the check failures on Windows, it...