Hi Martin, I've just noticed that EBImage, which is on the list of packages not to be regenerated, is actually affected too (according to the output below). Therefore, I would like to ask to have it regenerated for the sake of clean commit history.
Thanks, Andrzej [oles@localhost EBImage]$ git log --all --committer="unknown" --oneline d3e3542 Bumped version numbers for BioC 2.7 trunk 5b5fede git-svn-id: file:///home/git/ hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/EBImage@46404 bc3139a8-67e5-0310-9ffc-ced21a209358 3146d06 Bumped version numbers for BioC 2.6 release e4a3134 Package version bump for BioC 2.6 devel. 79137d5 git-svn-id: file:///home/git/ hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_5/madman/Rpacks/EBImage@42685 bc3139a8-67e5-0310-9ffc-ced21a209358 cf471ff Package version bump for BioC 2.5 release. df1d2a5 Bumped pkg versions for BioC 2.5 devel line. 307e349 git-svn-id: file:///home/git/ hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/EBImage@39014 bc3139a8-67e5-0310-9ffc-ced21a209358 43efe5d Bumped pkg versions for BioC 2.4 release. 446dc82 git-svn-id: file:///home/git/ hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/EBImage@34828 bc3139a8-67e5-0310-9ffc-ced21a209358 4362984 Bumping version numbers for BioC 2.4 devel. 1e8d268 Bumping version numbers for BioC 2.3 release. 1a0f09f Updating the version number for the trunk post-BioC 2.2 release. 53ffd85 Create release branch for BioC 2.2. 5650568 Updating the version number for the BioC 2.2 release. 7763cc0 Remove unused BioConductor build options file. b67438e JWM:Added biocViews On Mon, Aug 21, 2017 at 11:54 PM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > On 08/21/2017 05:30 PM, Stephanie M. Gogarten wrote: > >> I was actually thinking of SeqVarTools, since I have local commits that >> I'm not ready to push yet. GENESIS and GWASdata could be put on the "do not >> regenerate" list also - they have no unknown users, and I'd rather not go >> through all the steps again if I don't have to. >> > > I did > > SeqVarTools$ git log --all --committer="unknown" --oneline > SeqVarTools$ > > so there are no unknown commits. We won't regenerate. > > For those following along at home :) there are false positives from the > above, e.g., in Biobase where there really was no known user... > > Biobase$ git log --all --committer="unknown" |grep -B 3 cvs2svn > Author: unknown <unknown@email> > Date: Mon Aug 23 17:00:07 2004 +0000 > > This commit was manufactured by cvs2svn to create branch 'RELEASE_1_4'. > > > Martin > > >> thanks, >> Stephanie >> >> On 8/21/17 1:23 PM, Martin Morgan wrote: >> >>> On 08/21/2017 03:17 PM, Stephanie M. Gogarten wrote: >>> >>>> If we followed the steps here: >>>> https://www.bioconductor.org/developers/how-to/git/maintain- >>>> github-bioc/ >>>> >>>> How much, if any, of this will need to be redone after the repositories >>>> are regenerated? In particular, if I don't have an unknown user, will the >>>> regenerated commits be equal to the previous commits, or will "git fetch >>>> upstream" duplicate my commit history? >>>> >>> >>> Hi Stephanie -- >>> >>> if there are no unknown users, then we should not regenerate your git >>> repository. Is this GWAStools? If so let's leave it on the list of >>> repositories not to regenerate? >>> >>> Martin >>> >>> >>> >>>> thanks, >>>> Stephanie >>>> >>>> On 8/21/17 9:00 AM, Martin Morgan wrote: >>>> >>>>> Hi git transitioners -- >>>>> >>>>> We'd like to regenerate git repositories from svn. This is because >>>>> some svn user ids were mapped to 'unknown' git users, so that contributors >>>>> would not be credited accurately. This will invalidate any local clones >>>>> made from git.bioconductor.org. >>>>> >>>>> Our plan is to regenerate all git repositories EXCEPT those that have >>>>> been modified when we are ready (probably tomorrow morning). Modified >>>>> repositories that we would NOT regenerate, based on current commits, are >>>>> listed below; repositories modified between now and when we are ready to >>>>> update would also NOT be regenerated: >>>>> >>>>> beadarray BiocStyle CAMERA Cardinal CEMiTool ChemmineR cydar cytofkit >>>>> derfinder derfinderHelper derfinderPlot DmelSGI DOSE EBImage ELMER >>>>> ensembldb FamAgg gcapc GenVisR ggtree GOexpress gQTLstats GWASTools >>>>> isomiRs >>>>> karyoploteR LOBSTAHS motifcounter piano Rdisop REMP Rhdf5lib rnaseqcomp >>>>> seqplots systemPipeR TCGAbiolinks TCGAbiolinksGUI vsn >>>>> >>>>> >>>>> For a little more detail, the problem is manifest as 'unknown' authors >>>>> in a git commit, e.g., in Biobase from svn user 'jmc' >>>>> >>>>> commit b5ae43bc8aae967b80062da13e5085a6a305b274 >>>>> Author: unknown <unknown> >>>>> Date: Fri Dec 7 15:17:06 2001 +0000 >>>>> >>>>> fixed the arguments to 'show' methods >>>>> >>>>> >>>>> A more common problem is that the git author 'name' is 'unknown', as >>>>> in this limma commit >>>>> >>>>> commit 5910dc34a952a72816ada787d3f2c849edf48a95 >>>>> Author: unknown <sm...@wehi.edu.au> >>>>> Date: Tue Jul 25 07:23:39 2017 +0000 >>>>> >>>>> >>>>> >>>>> The problem primarily affects users with svn accounts from the earlier >>>>> part of Bioconductor's svn history, and stems from incomplete historical >>>>> records about the user name associated with svn accounts (this information >>>>> is not stored in svn per se). >>>>> >>>>> Please feel free to respond here if your package is listed above but >>>>> you would like it to be regenerated anyway; remember that you will loose >>>>> any commits made, and invalidate your local repository. >>>>> >>>>> Sorry for the inconvenience, >>>>> >>>>> Martin >>>>> >>>>> >>>>> This email message may contain legally privileged >>>>> and/or...{{dropped:2}} >>>>> >>>>> _______________________________________________ >>>>> Bioc-devel@r-project.org mailing list >>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>>> >>>> >>> >>> This email message may contain legally privileged and/or confidential >>> information. If you are not the intended recipient(s), or the employee or >>> agent responsible for the delivery of this message to the intended >>> recipient(s), you are hereby notified that any disclosure, copying, >>> distribution, or use of this email message is prohibited. If you have >>> received this message in error, please notify the sender immediately by >>> e-mail and delete this email message from your computer. Thank you. >>> >> > > This email message may contain legally privileged and/or...{{dropped:2}} > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
