[Bioc-devel] RMassBank (almost) builds ...

Egon Willighagen egon.willighagen at gmail.com
Thu Oct 13 16:47:24 CEST 2016

Hi all, including all BioC developers,

On Thu, Oct 13, 2016 at 4:32 PM, Zach Charlop-Powers
<zach.charlop.powers at gmail.com> wrote:
> When I initially submitted to CRAN I did NOT check the Java version and
> therefore users would be able to use Java 7 and would encounter errors only
> when using some features of Depict.  But in going through the submission
> gauntlet I was asked to add a system requirement and a check for the Java
> version. In retrospect a warning may have been more appropriate.

John May told me that it only depends on J7, but maybe one of the CDK
dependencies now depends on J8?

> In terms of fixing this issue, I would mention that the single biggest
> problem in uploading to CRAN is that the CDK JAR size is much bigger
> (~18mb?)

No, more like 25MB :)

> than the maximum allowed size (~5mb).

Ah... well, it's mostly dependencies that increase the size.

BioC developers, would rcdk be welcome on BioConductor? It's
frequently used in biology, e.g. metabolomics.

Rajarshi, Zach, would you consider that if the size issue becomes an issue?

Alternative, the whole CDK modularization has the purpose of being
able to reduce the size of the needed libs. We could look and see
which CDK modules are actually used by rcdk and then not depend on the
full CDK but only on the modules it really needs.

> I was given a waiver when I argued that the CDK core libraries are updated only infrequently.

That only makes sense of you put the CDK dependencies in rcdk-libs, or
possible split up in three versions, because the 3rd party libs the
CDK depends on are more stable than the CDK, which has releases every
half year or so at this moment. I think if you put the 3rd party lib
jars in rcdk-libs and the CDK jars in rcdk itself, you may still be
below the 5MB...

> I think it
> would be very nice to have more rapid updates of rCDK on CRAN that tracks
> the CDK releases but this would require a better way to load JARs on CRAN as
> the package size was a friction point. For comparison, many rJava packages
> use only a few Java files that boil down to small Jars of <1Mb.  The admins
> were understandably concerned about the strain on the archive system of
> large JARs.

Yes, I know this issue, which I had with the rrdf package too. (BioC
developers, would that package be welcome on BioConductor?)


E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
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ORCID: 0000-0001-7542-0286
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