[Bioc-devel] groHMM package error
I don't see a valid version bump? If there is no version bump, then it will not propagate on our system Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263
From: Tulip Nandu <Tulip.Nandu at UTSouthwestern.edu>
Sent: Thursday, December 5, 2024 12:25 PM
To: Kern, Lori <Lori.Shepherd at RoswellPark.org>; James W. MacDonald <jmacdon at uw.edu>; Mike Smith <grimbough at gmail.com>
Cc: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] groHMM package error
Sent: Thursday, December 5, 2024 12:25 PM
To: Kern, Lori <Lori.Shepherd at RoswellPark.org>; James W. MacDonald <jmacdon at uw.edu>; Mike Smith <grimbough at gmail.com>
Cc: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] groHMM package error
Hi, I have updated the groHMM developer's version with the edits suggested by Mike on decideTests() for edgeR. Hopefully it should work smoothly now. Let me know if anything else needs to be done from my end. Thank you everyone for your prompt response and help. Regards, Tulip. ________________________________ From: Kern, Lori <Lori.Shepherd at RoswellPark.org> Sent: Thursday, December 5, 2024 5:50 AM To: Tulip Nandu <Tulip.Nandu at UTSouthwestern.edu>; James W. MacDonald <jmacdon at uw.edu>; Mike Smith <grimbough at gmail.com> Cc: bioc-devel at r-project.org <bioc-devel at r-project.org> Subject: Re: [Bioc-devel] groHMM package error So the command that fails: git push origin master If we break down the command, it loosely is saying push to the remote listed as origin to the branch designation master and I'm on a branch called master (implied) Looking at your origin remote: origin git at github.com:Kraus-Lab/groHMM.git That is to your own or your labs github. This has nothing to do with Bioconductor permissions but that on the github. You will have to look into how to resolve this on github. The upstream remote is the Bioconductor location of the package. upstream git at git.bioconductor.org:packages/groHMM.git That being said, what is the name of the branch you are locally on? Based on the first call, I will assume master. Bioconductor no longer uses a master branch. Our default, devel branch is now named devel. See https://contributions.bioconductor.org/branch-rename-faqs.html<https://secure-web.cisco.com/1Yfvx2WnlOA1-38OJC-f0s4hSAHSe4sZkNnrIKdpH2wM_gJuv27zWUile0Z-RmXGIjoCdoW2MaeZCmK-OsKv1ECgOebY_zY5bBbWswxfeHJwHaCOT0IlkjQsFH-eoDyQsLOjy1ADUuSoMc75wdyphtMTJda7oeISvZfj1_2Wvb2mCv20wupKPdUWtwOfwY3Xum0bfogIjm_6NcgiFOyfHIFTK3LpWcEiBAjz3fqzbk9maKc21qrIJcP2d2YuT5Kb1Jq1sYcL3WzHamPBH8Jh0xd-fLZ-sbD58SZyrx9ydc9GK9NvPD3ukW6z2fDZCCnlo/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fcontributions.bioconductor.org%2Fbranch-rename-faqs.html__%3B%21%21MznTZTSvDXGV0Co%21G7xDI5mCtpNfI2_kxFf5jzrWJu0CJwPadHg-eh5tOD5mldEz7G7LeKTWfRVvENVHu8qk4RsBDQ9uu4IYueMoIF41rmTVP6K6Gx5Nz9A%24> if your local branch is master you would do something like the following to push to git.bioconductor.org git push upstream master:devel essentially reading: push the changes to the remote listed as upstream. And push my local master branch to the remote devel branch. Cheers, Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ________________________________ From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Tulip Nandu <Tulip.Nandu at UTSouthwestern.edu> Sent: Wednesday, December 4, 2024 5:23 PM To: James W. MacDonald <jmacdon at uw.edu>; Mike Smith <grimbough at gmail.com> Cc: bioc-devel at r-project.org <bioc-devel at r-project.org> Subject: Re: [Bioc-devel] groHMM package error Hi, Thank you for your earlier message. tulipnandu at tulips-mbp groHMM % git remote -v origin git at github.com:Kraus-Lab/groHMM.git (fetch) origin git at github.com:Kraus-Lab/groHMM.git (push) upstream git at git.bioconductor.org:packages/groHMM.git (fetch) upstream git at git.bioconductor.org:packages/groHMM.git (push) After that: I keep getting this error message: tulipnandu at tulips-mbp groHMM % ssh -T git at github.com git at github.com: Permission denied (publickey). I have added the key to the github account on BioHPC. Another message I receive: tulipnandu at tulips-mbp groHMM % git push origin master git at github.com: Permission denied (publickey). fatal: Could not read from remote repository. Please make sure you have the correct access rights and the repository exists. tulipnandu at tulips-mbp groHMM % I have made the changes to the git repository at our end. Can you please help me? Regards, Tulip. ________________________________ From: James W. MacDonald <jmacdon at uw.edu> Sent: Tuesday, December 3, 2024 2:31 PM To: Tulip Nandu <Tulip.Nandu at UTSouthwestern.edu>; Mike Smith <grimbough at gmail.com> Cc: bioc-devel at r-project.org <bioc-devel at r-project.org> Subject: RE: [Bioc-devel] groHMM package error You need to commit your changes to git at git.bioconductor.org, which you apparently have not done as yet (you should have git at 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.wokaty at 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://secure-web.cisco.com/16_v9KvAnSn5NTE4bTiw78EKac1H9ipCVrD15qZr6e0WzggraBQhvfCSIwCLL-NpPpZOxGuzdCoG2QFSZYXUfh02U187DGSNi9GMRoeItGMXmL8Pxv6E1PaofrESKPYKGpKLAAQRczRO1tuXb1oM7q8ahoI5VlJUWZ16K09Ns6efVylSfGwcX3p0elHPzeH8nJ3FihmzlQHBZDYp0wHTwfeGkDBzeGOnqCuaTo92X12THhrzDkwVex8p5FJhW38JXKuMXH9g3J2-jcnq_tqak_SBvoa5WjbL36eOfKKNQpyaUSLEOjiwh6OIg-mYmQ0yx/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fcontributions.bioconductor.org%2Fgit-version-control.html__;!!MznTZTSvDXGV0Co!D1Ec1At0koOWiqp-WDw8kmv5F2XS6u9FgDh9_6bOg6sahspYVpDQH4VMAWnhLzWraEuUptCNTFhuhD3a6ZVoPFJgJ1w$<https://secure-web.cisco.com/1GWLgYnV8zmTyLvVUS6dbRWiraO1NBwG4uVx53Xa1mLCraomRypq5LJ0XEcOwrW3zlkizyb7oAw0gRRC5ZrZISZyvTlsNn0Q_8ld-oxHBg791VEFq3hPjx_gaQyGLutwqq1teoujTwXzTMHkzYp6bqJYTZw8eXvLQGhY78ojU-xIi0Vtdn69ioMDV-w-9v2geDPW7lW09eQdm6YwOXSqgfZ86vdRumg6AqtrRjFYqYXUezvyEaPvWj36dUU51wCmu_mYkR4YJVn9m0khwwGYzRvVkyTyWcen8EUyM8Y9lqj55PmkZsdYEzNEBjaMJ-9xh/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F16_v9KvAnSn5NTE4bTiw78EKac1H9ipCVrD15qZr6e0WzggraBQhvfCSIwCLL-NpPpZOxGuzdCoG2QFSZYXUfh02U187DGSNi9GMRoeItGMXmL8Pxv6E1PaofrESKPYKGpKLAAQRczRO1tuXb1oM7q8ahoI5VlJUWZ16K09Ns6efVylSfGwcX3p0elHPzeH8nJ3FihmzlQHBZDYp0wHTwfeGkDBzeGOnqCuaTo92X12THhrzDkwVex8p5FJhW38JXKuMXH9g3J2-jcnq_tqak_SBvoa5WjbL36eOfKKNQpyaUSLEOjiwh6OIg-mYmQ0yx%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2F%2A2Fcontributions.bioconductor.org%2A2Fgit-version-control.html__%3B%21%21MznTZTSvDXGV0Co%21D1Ec1At0koOWiqp-WDw8kmv5F2XS6u9FgDh9_6bOg6sahspYVpDQH4VMAWnhLzWraEuUptCNTFhuhD3a6ZVoPFJgJ1w%24__%3BJSUlJSUlJSUl%21%21MznTZTSvDXGV0Co%21G7xDI5mCtpNfI2_kxFf5jzrWJu0CJwPadHg-eh5tOD5mldEz7G7LeKTWfRVvENVHu8qk4RsBDQ9uu4IYueMoIF41rmTVP6K6zQuhDZQ%24> -----Original Message----- From: Bioc-devel <bioc-devel-bounces at r-project.org> On Behalf Of Tulip Nandu Sent: Tuesday, December 3, 2024 3:14 PM To: Mike Smith <grimbough at gmail.com> Cc: bioc-devel at 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 <grimbough at gmail.com> Sent: Tuesday, November 26, 2024 2:50 AM To: Tulip Nandu <Tulip.Nandu at UTSouthwestern.edu> Cc: bioc-devel at r-project.org <bioc-devel at 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://secure-web.cisco.com/1l4IXc7KdLp5eV00Nm_hQoy6Gk6XDiPosw64Iwbq_av3U6heY7PCBd3SXPirzNs0zT0xlkKrDXTNUg6-MDVzYtGvJhGSgKT9tMzL7-YHa5U9uKytV3jkX6wqVpRApTsmDBIEGNQeRggFExswQF9YAQOiqgWbapncK3zYZuq4mZ8VBwR-RB09_MRo8JkVl2k8kR2EiRbXaRJUp3si4q4dW4OQv9UpxMlBjjSitWPhD_5whHeJlyKitOLE_fYlSSOGyOM35LDGnLtj9_Der0ckR7qNYmAvyiXsh0VbLmTx_fFfEpWupZK4dZNqV_k9MVmd7/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fnews%2FedgeR%2FNEWS__;!!K-Hz7m0Vt54!ml36G27n5i71mmZqYh9kGx64fb8MnMWqcgTRb-IOUtzTvcuIr8z00917gwIae3eKB558z662Sqs-Iu35-pnRAO0wmBtwCQ$<https://secure-web.cisco.com/1rs97dRszuJ_pxsw65lMxAyi5pvoVHkXOgd7RoWIUNGgea3vDuzMU6Uh9JfMwAIX43hd2ycpQypaGN36MvvZa9qoRJ30fVRG85v6yoQiX5p3MKyWSPUVfI_cprONmAFIR-tIcxSg6iDOWBvjnmbgxD_n0p-PRJXfRmTcZ5aKQpq9NIsvZtRnIPl2ZtKM1Ixjt5j2J0G22w8BBH5vXFlkkRKchRnwmQ8f-sESIrHWZYku3tednS8X62PwoRmtEbnrgkvTe6fO2EE9wsJkwGFxPRDvXCplBw2QZ5f3WFH_9z4n6us2Rybi8MYML_o36YF-n/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1l4IXc7KdLp5eV00Nm_hQoy6Gk6XDiPosw64Iwbq_av3U6heY7PCBd3SXPirzNs0zT0xlkKrDXTNUg6-MDVzYtGvJhGSgKT9tMzL7-YHa5U9uKytV3jkX6wqVpRApTsmDBIEGNQeRggFExswQF9YAQOiqgWbapncK3zYZuq4mZ8VBwR-RB09_MRo8JkVl2k8kR2EiRbXaRJUp3si4q4dW4OQv9UpxMlBjjSitWPhD_5whHeJlyKitOLE_fYlSSOGyOM35LDGnLtj9_Der0ckR7qNYmAvyiXsh0VbLmTx_fFfEpWupZK4dZNqV_k9MVmd7%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2F%2A2Fbioconductor.org%2A2Fpackages%2A2Frelease%2A2Fbioc%2A2Fnews%2A2FedgeR%2A2FNEWS__%3B%21%21K-Hz7m0Vt54%21ml36G27n5i71mmZqYh9kGx64fb8MnMWqcgTRb-IOUtzTvcuIr8z00917gwIae3eKB558z662Sqs-Iu35-pnRAO0wmBtwCQ%24__%3BJSUlJSUlJSUlJSUlJSU%21%21MznTZTSvDXGV0Co%21G7xDI5mCtpNfI2_kxFf5jzrWJu0CJwPadHg-eh5tOD5mldEz7G7LeKTWfRVvENVHu8qk4RsBDQ9uu4IYueMoIF41rmTVP6K6q-G62nk%24> <https://secure-web.cisco.com/1l4IXc7KdLp5eV00Nm_hQoy6Gk6XDiPosw64Iwbq_av3U6heY7PCBd3SXPirzNs0zT0xlkKrDXTNUg6-MDVzYtGvJhGSgKT9tMzL7-YHa5U9uKytV3jkX6wqVpRApTsmDBIEGNQeRggFExswQF9YAQOiqgWbapncK3zYZuq4mZ8VBwR-RB09_MRo8JkVl2k8kR2EiRbXaRJUp3si4q4dW4OQv9UpxMlBjjSitWPhD_5whHeJlyKitOLE_fYlSSOGyOM35LDGnLtj9_Der0ckR7qNYmAvyiXsh0VbLmTx_fFfEpWupZK4dZNqV_k9MVmd7/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fnews%2FedgeR%2FNEWS__;!!MznTZTSvDXGV0Co!BCGS40g3d3SSGednQhbxHgpWzGAsYc9EsCe70-JZ9IXVg3a8PO-zA19gV1ChkR4Rh_ekHivdYDmFEO8pn_DJEQx-jd1t$<https://secure-web.cisco.com/1fBRHHbYECjY89CURsF9k9rJ3tSOqHwaikc6bN7QMlV7NcQk0XWZzigbp89h5S4xFKVbLfMySP53XqCFokWptemrt4zqqUMUlvzoIwxhCZZu2oqkoAAzk7uauK0Re6P8SNgzzW_tZAZK8cWjij3ymVwo6uHW4DsobVrgCw_CIqfEFlnfhI9vnQO66v_a8mBgpb9A4P5iuKHo22knqejXIm2QdfFFvZhb9CejyABLgDOfcDEIntWjJ27S11xL5Te0Y14lDwWfEWHb33rAvxRGB8V3nxYMc77HFISGp232Aa7lEUYuuFGLHnkEMHuvZTuw4/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1l4IXc7KdLp5eV00Nm_hQoy6Gk6XDiPosw64Iwbq_av3U6heY7PCBd3SXPirzNs0zT0xlkKrDXTNUg6-MDVzYtGvJhGSgKT9tMzL7-YHa5U9uKytV3jkX6wqVpRApTsmDBIEGNQeRggFExswQF9YAQOiqgWbapncK3zYZuq4mZ8VBwR-RB09_MRo8JkVl2k8kR2EiRbXaRJUp3si4q4dW4OQv9UpxMlBjjSitWPhD_5whHeJlyKitOLE_fYlSSOGyOM35LDGnLtj9_Der0ckR7qNYmAvyiXsh0VbLmTx_fFfEpWupZK4dZNqV_k9MVmd7%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2F%2A2Fbioconductor.org%2A2Fpackages%2A2Frelease%2A2Fbioc%2A2Fnews%2A2FedgeR%2A2FNEWS__%3B%21%21MznTZTSvDXGV0Co%21BCGS40g3d3SSGednQhbxHgpWzGAsYc9EsCe70-JZ9IXVg3a8PO-zA19gV1ChkR4Rh_ekHivdYDmFEO8pn_DJEQx-jd1t%24__%3BJSUlJSUlJSUlJSUlJSU%21%21MznTZTSvDXGV0Co%21G7xDI5mCtpNfI2_kxFf5jzrWJu0CJwPadHg-eh5tOD5mldEz7G7LeKTWfRVvENVHu8qk4RsBDQ9uu4IYueMoIF41rmTVP6K6NNxfGiM%24>> 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.Nandu at utsouthwestern.edu<mailto:Tulip.Nandu at 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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