Hi Tulip, I'm glad you are maintaining groHMM; I previously had not got much response from contributing bug fixes, so you may be interested in looking at and maybe integrating my fork: https://github.com/coregenomics/groHMM where the NEWS file summarizes the changes. There is also a test suite that checks more behaviors than the vignette successfully building.
Pariksheet ________________________________________ From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of James W. MacDonald <jmac...@uw.edu> Sent: Tuesday, December 3, 2024 3:31 PM To: Tulip Nandu; Mike Smith Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] groHMM package error [You don't often get email from jmac...@uw.edu. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] You need to commit your changes to g...@git.bioconductor.org, which you apparently have not done as yet (you should have g...@git.bioconductor.org set up as a remote which you can see by doing git remote -v). The last commit is Jennifer Wokaty bumping the version for the last release: /groHMM$ git log commit a68457648cdef96ae2a8f40c484496e935d0fcb3 (HEAD -> devel, origin/master, origin/devel, origin/HEAD) Author: J Wokaty <jennifer.wok...@sph.cuny.edu> Date: Tue Oct 29 09:56:11 2024 -0400 bump x.y.z version to odd y following creation of RELEASE_3_20 branch You also need to bump the version number in order to get the new version to build. You also need to make changes to the RELEASE_3_20 branch if you want the fix to propagate to the release version of your package. Please see the git version control section of the development pages https://contributions.bioconductor.org/git-version-control.html -----Original Message----- From: Bioc-devel <bioc-devel-boun...@r-project.org> On Behalf Of Tulip Nandu Sent: Tuesday, December 3, 2024 3:14 PM To: Mike Smith <grimbo...@gmail.com> Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] groHMM package error Hi, I edited the file based on Mike' s suggestion on the git page (image1) but doesn't seem to reflect when I clone the file using the git clone bioconductor package yet. Can someone confirm it will be done and nothing else I have to do from my end. Let me know. Regards, Tulip. ________________________________ From: Mike Smith <grimbo...@gmail.com> Sent: Tuesday, November 26, 2024 2:50 AM To: Tulip Nandu <tulip.na...@utsouthwestern.edu> Cc: bioc-devel@r-project.org <bioc-devel@r-project.org> Subject: Re: [Bioc-devel] groHMM package error EXTERNAL MAIL Dear Tulip, The decideTestsDGE() function was deprecated in edgeR 4.2 and removed in the new 4.4 release. You can find some notes ion this n the NEWS at https://urldefense.com/v3/__https://bioconductor.org/packages/release/bioc/news/edgeR/NEWS__;!!K-Hz7m0Vt54!ml36G27n5i71mmZqYh9kGx64fb8MnMWqcgTRb-IOUtzTvcuIr8z00917gwIae3eKB558z662Sqs-Iu35-pnRAO0wmBtwCQ$ <https://urldefense.com/v3/__https://bioconductor.org/packages/release/bioc/news/edgeR/NEWS__;!!MznTZTSvDXGV0Co!BCGS40g3d3SSGednQhbxHgpWzGAsYc9EsCe70-JZ9IXVg3a8PO-zA19gV1ChkR4Rh_ekHivdYDmFEO8pn_DJEQx-jd1t$> It looks to me like you should be able to use decideTests() as a drop in replacement in your package. Best, Mike On Mon, 25 Nov 2024 at 23:23, Tulip Nandu <tulip.na...@utsouthwestern.edu<mailto:tulip.na...@utsouthwestern.edu>> wrote: Hi, I keep getting this message from Bioconductor for groHMM package and don't know what the error is since I haven't changed anything in the package. Can someone please help? Regards, Tulip. "Warning in makeConsensusAnnotations(kgChr7, keytype = "gene_id", mc.cores = getOption("mc.cores")) : 562 ranges do not have gene_id and they are dropped Reduce isoforms(701) ... OK Truncate overlapped ranges ... OK 'select()' returned 1:1 mapping between keys and columns Calculate overlapping ... OK Scale overlapping ... OK Warning: file stem ‘/home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpkfITSx/Rbuild130dca6dd2fd85/groHMM/vignettes/groHMM-fig2’ is not portable Calculate overlapping ... OK Scale overlapping ... OK Loading required package: limma Attaching package: ‘limma’ The following object is masked from ‘package:BiocGenerics’: plotMA Error: processing vignette 'groHMM.Rnw' failed with diagnostics: chunk 21 (label = DE for trascripts) Error in decideTestsDGE(et, p = 0.001, adjust = "fdr") : could not find function "decideTestsDGE" --- failed re-building ‘groHMM.Rnw’ SUMMARY: processing the following file failed: ‘groHMM.Rnw’ Error: Vignette re-building failed. Execution halted" ________________________________ UT Southwestern Medical Center The future of medicine, today. 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