[Bioc-devel] BiocManager now on CRAN

[Gabe Becker]

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.

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> 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")
> README.md:53:biocLite("ClusterSignificance")
> README.Rmd:45:source("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
>
> 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>> wrote:
> >>
> >>> biocLite
> >
>
>
>
> 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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