[Bioc-devel] Package size note

Kasper Daniel Hansen k@@perd@nielh@n@en @ending from gm@il@com
Tue May 15 09:59:15 CEST 2018


Kenneth,

You should _always_ run R CMD check (and R CMD BiocCheck) on the tarball
generated by R CMD build.  The build step essentially cleans the code.  If
your vignette takes a bit to generate (the vignette gets generated with R
CMD build), just do R CMD build --no-build-vignettes

Best,
Kasper

On Tue, May 15, 2018 at 9:41 AM, Kenneth Condon <roonysgalbi at gmail.com>
wrote:

> Hi Lori,
>
>
> Thanks for the reply. The actual tar.gz built by R CMD build is only 3Mb so
> maybe I should ignore the note and submit? The note may actually be
> referring to large .git objects in the git history - not sure.
>
> Regards,
> Kenneth
>
> On Mon, May 14, 2018 at 12:15 PM, Shepherd, Lori <
> Lori.Shepherd at roswellpark.org> wrote:
>
> >
> > Please review the package guidelines -
> >
> >
> > http://bioconductor.org/developers/package-guidelines/
> >
> >
> > Generally, Bioconductor will insist that the R CMD built package tar.gz
> be
> > less than 4MB for software packages (There are some exceptions for data
> > experiment or annotation packages).
> >
> >
> > If this is a software packages,  there are a few options
> >
> >
> > With large data files:
> >
> > 1.  Reduce the size of the data.  A full data set is often not needed to
> > display the functionality and utility of a package.  A reduced smaller
> > subset of data is recommended
> >
> > 2.  See if there is already existing data available in one of the data
> > experiment packages or experimenthub that can be used instead of
> providing
> > new data.
> >
> > 3. separate out the data files into a separate associate data
> > experiment package or use the experimenthub to store data.
> >
> >
> >
> > Are you generating or providing a lot of static image files for the
> > vignette?  There might also be some opportunity to reduce the size but
> have
> > images generated automatically if this is the case.
> >
> >
> >
> >
> >
> > Lori Shepherd
> >
> > Bioconductor Core Team
> >
> > Roswell Park Cancer Institute
> >
> > Department of Biostatistics & Bioinformatics
> >
> > Elm & Carlton Streets
> >
> > Buffalo, New York 14263
> > ------------------------------
> > *From:* Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of
> > Kenneth Condon <roonysgalbi at gmail.com>
> > *Sent:* Saturday, May 12, 2018 6:23:02 PM
> > *To:* bioc-devel
> > *Subject:* [Bioc-devel] Package size note
> >
> > Hi all,
> >
> > I almost have a clean R CMD check.
> >
> > R CMD check results0 errors | 0 warnings | 1 note checking installed
> > package size ... NOTE
> >   installed size is  6.1Mb
> >   sub-directories of 1Mb or more:
> >     data   3.0Mb
> >     doc    2.9Mb
> >
> >
> > Firstly, do I need to get this below 5Mb?
> >
> > Secondly, I don't have a sub-directory called 'doc' - what is this?
> >
> > Regards,
> > Kenneth
> >
> >         [[alternative HTML version deleted]]
> >
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