[Bioc-devel] BiocManager now on CRAN

[Marcel Ramos]

Hi Leo,

Thanks for bringing that up and making those changes.
We wanted to emphasize software packages first and then address experiment
data and workflow packages since they are fewer anyhow.

I will be adding those as additional files in the gist.

To update experiment data packages, the commands are the same as if
you were updating a software package.

I will check with the rest of the team about modifying workflow packages
so watch this space.

Regards,

Marcel

PS. See short reponse below.


On 07/24/2018 03:15 PM, Leonardo Collado Torres wrote:
> 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.
I've checked on this and the packages that use `biocValid` intersect with
those that use `BiocInstaller|biocLite`. Thanks.
> 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...
>>> _______________________________________________
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>>>
>>
>>
>> --
>> Gabriel Becker, Ph.D
>> Scientist
>> Bioinformatics and Computational Biology
>> Genentech Research
>>
>>          [[alternative HTML version deleted]]
>>
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>



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