[Bioc-devel] CRAN package with Bioconductor dependencies

[Martin Morgan]

On 03/02/2015 03:22 PM, Ryan C. Thompson wrote:
> I thought CRAN packages weren't allowed to depend on Bioconductor packages for
> exactly this reason.

CRAN packages can and do depend on Bioconductor packages.

The different versioning schemes use by CRAN and by Bioconductor can lead to 
confusion, and can end in tears.

My advice is to use, and tell your users to use, biocLite() for everything 
(including, in devel, github, e.g., biocLite("mtmorgan/biocdb"), which delegates 
to devtools).

Martin

>
> On 03/02/2015 03:18 PM, Laurent Gatto wrote:
>> Dear all,
>>
>>
>> I had never realised that CRAN packages that depended on Bioc packages
>> could actually not be installed with install.packages without setting a
>> repo or using BiocInstaller::bioLite. Here is an example using a fresh R
>> installation
>>
>>    http://cran.r-project.org/web/packages/MSeasy/index.html
>>    Depends: amap, clValid, cluster, fpc, mzR, xcms
>>
>> $ docker run --rm -ti rocker/r-base R
>>
>> R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
>> Copyright (C) 2014 The R Foundation for Statistical Computing
>> Platform: x86_64-pc-linux-gnu (64-bit)
>>
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>> You are welcome to redistribute it under certain conditions.
>> Type 'license()' or 'licence()' for distribution details.
>>
>>    Natural language support but running in an English locale
>>
>> R is a collaborative project with many contributors.
>> Type 'contributors()' for more information and
>> 'citation()' on how to cite R or R packages in publications.
>>
>> Type 'demo()' for some demos, 'help()' for on-line help, or
>> 'help.start()' for an HTML browser interface to help.
>> Type 'q()' to quit R.
>>
>>> install.packages("MSeasy")
>> Installing package into ‘/usr/local/lib/R/site-library’
>> (as ‘lib’ is unspecified)
>> Warning: dependencies ‘mzR’, ‘xcms’ are not available
>> also installing the dependencies ‘modeltools’, ‘DEoptimR’, ‘mclust’,
>> ‘flexmix’, ‘prabclus’, ‘diptest’, ‘mvtnorm’, ‘robustbase’, ‘kernlab’,
>> ‘trimcluster’, ‘amap’, ‘clValid’, ‘fpc’
>>
>> [...]
>>
>> ERROR: dependencies ‘mzR’, ‘xcms’ are not available for package ‘MSeasy’
>> * removing ‘/usr/local/lib/R/site-library/MSeasy’
>>
>> The downloaded source packages are in
>>     ‘/tmp/Rtmp4T40ub/downloaded_packages’
>> Warning message:
>> In install.packages("MSeasy") :
>>    installation of package ‘MSeasy’ had non-zero exit status
>>
>> This does sound really counter-intuitive. Am I missing anything?
>>
>> Laurent
>>
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>
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