[Bioc-devel] CRAN package with Bioconductor dependencies

[Laurent Gatto]

Thank you all for your answers.

Laurent

On  2 March 2015 23:27, Martin Morgan wrote:

> 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?
>
> biocLite("MSeasy") is easy and works.
>
> Otherwise yes, to install a Bioconductor package using install.packages() 
> requires that you've selected (via chooseBioCmirror() or options("BioC_mirror")) 
> or provided (e.g., install.packages("MSeasy", 
> repos=BiocInstaller::biocinstallRepos()) a Bioconductor repository.
>
> Since the mirror choices provided by chooseBioCmirror() are hard-wired, users of 
> R3.0.0 + chooseBioCmirror() will get an older version of Biocondcutor than users 
> of 3.0.0 + biocLite().
>
> Martin
>
>>
>> Laurent
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>

-- 
Laurent Gatto
http://cpu.sysbiol.cam.ac.uk/