Hi Marcel, I noticed that https://gist.github.com/LiNk-NY/44cc844a169d5d96c777a69037dae653 doesn't include the experiment data and workflow packages. I updated mine preemptively (derfinderData and recountWorkflow).
By the way, how do I sync experiment data package updates? I forgot how to do so. Maybe it's only via svn. I checked http://bioconductor.org/developers/how-to/git/ and the commit in question is https://github.com/leekgroup/derfinderData/commit/cc0a295a730f8f19a429f28c7b327ee15ccd1e81. Last time I did it was in 2015. Also, I suggest changing your grep command to: grep -rnE "biocLite|biocValid" * that way you can include biocValid() calls which now should be BiocManager::valid(). I had included several of them in my package vignettes. Best, Leo On Mon, Jul 16, 2018 at 1:06 PM Gabe Becker <becker.g...@gene.com> wrote: > > > Ah, of course. I should have realized that. Makes sense. I'll get that > fixed in devel soon. > > Thanks and sorry for the noise. > ~G > > On Mon, Jul 16, 2018 at 9:37 AM, Marcel Ramos <marcel.ra...@roswellpark.org> > wrote: > > > Hi Gabe, > > > > Please note that we are only making changes to packages in *bioc-devel*. > > > > BiocManager wouldn't fail for users with earlier versions of R because > > it doesn't apply to them. These users > > should be using the respective bioc-release versions and consequently > > `BiocInstaller`. > > > > BiocManger is currently supported only for `devel` and all /bioc-devel/ > > users have R 3.5.0 or greater going forward. > > > > > > Regards, > > Marcel > > > > > > On 07/16/2018 11:51 AM, Gabe Becker wrote: > > > Marcel et al, > > > > > > My genbankr package is one of the ones that mentions biocLite (in > > > README.md, actually, not the vignette proper, but still...). > > > Historically this was just because I had missed your email and hadn't > > > updated it, but when I sat down to do it I ran into an issue: > > > > > > BiocManager, while a huge step forward, requires R >3.5.0. That is > > > still relatively new, and my package (along with all Bioc packages > > > from the corresponding release) works fine under 3.4.x (and previous). > > > I'm somewhat loath to completely remove the biocLite based > > > instructions because install.packages("BiocManager") will fail (well, > > > not with an error, but it doesn't install anything...) for users with > > > earlier versions of R, wherease > > > source("http://bioconductor.org/biocLite.R") works and gets the > > > correct version for them IIRC. > > The `biocLite` instructions only apply the current and previous release > > versions of Bioconductor. > > > > > > Is there guidance on how to handle this issue? > > > > > > Thanks, > > > ~G > > > > > > On Sun, Jul 15, 2018 at 10:53 AM, Marcel Ramos > > > <marcel.ramospe...@roswellpark.org > > > <mailto:marcel.ramospe...@roswellpark.org>> wrote: > > > > > > Hi Jason, > > > > > > Please check all of your package files and not just the vignette. > > > > > > The criteria involve a simple `grep` search of all package files for > > > the words `biocLite` and `BiocInstaller`. > > > > > > ~/Bioconductor/ClusterSignificance (master) $ grep -rn "biocLite" * > > > README.md:52:source("https://bioconductor.org/biocLite.R > > > <https://bioconductor.org/biocLite.R>") > > > README.md:53:biocLite("ClusterSignificance") > > > README.Rmd:45:source("https://bioconductor.org/biocLite.R > > > <https://bioconductor.org/biocLite.R>") > > > README.Rmd:46:biocLite("ClusterSignificance") > > > > > > As I've mentioned in the previous emails, you can use: > > > > > > install.packages("BiocManager") > > > BiocManager::install("YourPackageNameHere") > > > > > > to replace the source function call. > > > > > > You may also refer to the "Installation" section of the devel > > > landing pages > > > for an additional example: > > > > > > http://bioconductor.org/packages/devel/bioc/html/ > > ClusterSignificance.html > > > <http://bioconductor.org/packages/devel/bioc/html/ > > ClusterSignificance.html> > > > > > > Best regards, > > > Marcel > > > > > > > > > On 07/14/2018 03:31 AM, Jason Serviss wrote: > > > > Hello Marcel, > > > > > > > > I notice that the package I maintain, ClusterSignificance, is > > > included > > > > in this list although I am unsure why. In your previous mail you > > > say: > > > > > > > >> After the next couple of weeks or so, we will be identifying > > > packages in > > > >> bioc-devel (3.8) that still > > > >> mention BiocInstaller / biocLite. > > > > > > > > I don’t find any mention of BiocInstaller or biocLite in the > > > > ClusterSignificance vignette and it is a bit unclear to me what > > > “make > > > > changes to their ... package code to support the use of > > > `BiocManager`” > > > > specifically entails. Would you mind expanding on what criteria, > > > other > > > > than usage of BiocInstaller or biocLite in the vignette, that might > > > > cause packages to appear in your gist? > > > > > > > > Kind Regards, > > > > Jason Serviss > > > > > > > > > > > >> On 13 Jul 2018, at 23:11, Marcel Ramos > > > >> <marcel.ramospe...@roswellpark.org > > > <mailto:marcel.ramospe...@roswellpark.org> > > > >> <mailto:marcel.ramospe...@roswellpark.org > > > <mailto:marcel.ramospe...@roswellpark.org>>> wrote: > > > >> > > > >>> biocLite > > > > > > > > > > > > > > > > This email message may contain legally privileged > > > and/or... > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > > -- > Gabriel Becker, Ph.D > Scientist > Bioinformatics and Computational Biology > Genentech Research > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel