[Bioc-devel] BiocManager now on CRAN
Leonardo Collado Torres
lcoll@do @ending from jhu@edu
Tue Jul 24 21:15:00 CEST 2018
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.gabe using 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.Ramos using 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.ramosperez using roswellpark.org
> > > <mailto:marcel.ramosperez using 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.ramosperez using roswellpark.org
> > > <mailto:marcel.ramosperez using roswellpark.org>
> > > >> <mailto:marcel.ramosperez using roswellpark.org
> > > <mailto:marcel.ramosperez using roswellpark.org>>> wrote:
> > > >>
> > > >>> biocLite
> > > >
> > >
> > >
> > >
> > > This email message may contain legally privileged
> > > and/or...
> >
> > _______________________________________________
> > Bioc-devel using 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]]
>
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