[Bioc-devel] CRAN package with Bioconductor dependencies

Hervé Pagès hpages at fredhutch.org
Tue Mar 3 00:32:31 CET 2015

Hi Laurent,

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?

I don't think you are. By default install.packages() doesn't know
about the BioC repos so...

But the CRAN builds do know about the BioC repos so CRAN packages
that depend on us do pass check (or not... but that's another story).

And sometimes we receive notifications from the CRAN maintainer that
some changes in our packages break some of their packages.

Also I'm not sure what version of BioC they depend on for their
builds. Our release schedules are different: 1 release per year
for them, 2 for us. If they use BioC release for their release builds,
then we can break CRAN packages when we release. It's unavoidable
I'm afraid.

Having CRAN packages that depend on us is just not a good situation


> Laurent
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
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