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.g...@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.ra...@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.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
>
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