[Bioc-devel] BiocManager now on CRAN

[Gabe Becker]

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...{{dropped:4}}
> >
> >     _______________________________________________
> >     Bioc-devel using r-project.org <mailto:Bioc-devel using r-project.org> mailing
> >     list
> >     https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >     <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
> >
> >
> >
> >
> > --
> > Gabriel Becker, Ph.D
> > Scientist
> > Bioinformatics and Computational Biology
> > Genentech Research
>
>
>
> This email message may contain legally privileged and/or...{{dropped:4}}
>
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>



-- 
Gabriel Becker, Ph.D
Scientist
Bioinformatics and Computational Biology
Genentech Research

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