[Bioc-devel] CRAN package with Bioconductor dependencies

[Gabe Becker]

Even if it is allowed, what is the reasoning behind not simply putting the
package in Bioconductor? It seems like a fair bit of pain for very little
benefit.

~G

On Mon, Mar 2, 2015 at 3:22 PM, Ryan C. Thompson <rct at thompsonclan.org>
wrote:

> I thought CRAN packages weren't allowed to depend on Bioconductor packages
> for exactly this reason.
>
>
> 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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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
> _______________________________________________
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>



-- 
Gabriel Becker, Ph.D
Computational Biologist
Genentech Research

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