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.ramospe...@roswellpark.org
>> <mailto:marcel.ramospe...@roswellpark.org>> wrote:
>>
>>> biocLite
>
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