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...{{dropped:4}}
>
> _______________________________________________
> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing
> list
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>
>
>
>
> --
> Gabriel Becker, Ph.D
> Scientist
> Bioinformatics and Computational Biology
> Genentech Research
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