[Bioc-devel] FW: RegEnrich problems reported in the Multiple platform build/check report for BioC 3.12

Dear Bioconductor Core Team, I was reported several days ago that my package (RegEnrich stable release version 1.0.0) had a problem in the building step. Then I fixed the bug and bumped the version number to 1.1.1, then I pushed the changes to GitHub and git.bioconductor.org. But today I still

Re: [Bioc-devel] ClusterJudge problems reported in the build/check

Did you remember to do a version bump when submitting the changes? It does not appear so. The build machines will not recognize code changes without a valid version bump. You should increase from 1.13.0 to 1.13.1 for the new changes to propagate and be available through BiocManager::install

[Bioc-devel] ClusterJudge problems reported in the build/check

Hi all, It seems that Bioconductor multi build/check does NOT use the updated git of ClusterJudge package. Here is the error reported: https://master.bioconductor.org/checkResults/3.12/bioc-LATEST/ClusterJudge/malbec1-checksrc.html However I fixed the error about a month ago and pushed the chang

Re: [Bioc-devel] Vignette compression

I guess it is mainly due to figures in the vignettes. Maybe you can use a smaller figure size, e.g. by setting `fig.width` in the vignettes? On Wed, 3 Mar 2021 at 13:50, Fabricio de Almeida < fabricio_almeidasi...@hotmail.com> wrote: > Sorry, I accidentally sent the incomplete email. > > With Bio

Re: [Bioc-devel] Moving minfi classes definition to a lighter package

hi, about a year ago we had a developer's forum session devoted to this subject, you might find useful the discussion we had starting on minute 29th here: https://www.youtube.com/watch?v=xsM4nN85cok part of the result of that discussion is in section 7 of this vignette: http://bioconductor.

Re: [Bioc-devel] Moving minfi classes definition to a lighter package

i advocated pkgnet and included a png but email seems to have been rejected On Wed, Mar 3, 2021 at 7:29 AM Kasper Daniel Hansen < kasperdanielhan...@gmail.com> wrote: > I am happy to engage in a discussion about this, although I'm not sure that > I am ultimately interested in having two packages

Re: [Bioc-devel] Vignette compression

Sorry, I accidentally sent the incomplete email. With BiocCheck::BiocCheck(), I get this: * Checking package size... 38 * ERROR: Package Source tarball exceeds Bioconductor size 39

[Bioc-devel] Vignette compression

Hi, all. I am testing my package on Windows, Linux and MacOS with GitHub Actions using biocthis. The package passes all checks with devtools::check(vignettes=FALSE) followed by BiocCheck::BiocCheck(), but when I build the vignettes, it exceeds the maximum package size. On building with devtool

Re: [Bioc-devel] Moving minfi classes definition to a lighter package

I am happy to engage in a discussion about this, although I'm not sure that I am ultimately interested in having two packages. But first I would like to look at some dependency graphs. I am wondering what makes the dependency tree this big (and my tree is smaller than yours, but still big: library

Re: [Bioc-devel] ExperimentHub package development - Windows OS specific error

Hey Gavin, You're right that built correctly! Strange I got the error yesterday considering I ran devtools::check_win_devel() Perhaps ExperimentHub doesn't update the snapshot automatically for this. Not to worry though, I think that is a headache for another day. Thanks again, Alan.

Re: [Bioc-devel] ExperimentHub package development - Windows OS specific error

I did not get this error on my Windows machine; ExperimentHub can find the alzzh_gwas_top100 dataset in Bioc 3.13 (devel). Your snapshot date is older than mine. R reported my snapshot date as "2021-03-02" Maybe you need to clear the cache? You can request all available snapshot dates with