From ligges at statistik.tu-dortmund.de  Sat Nov 13 17:49:08 2010
From: ligges at statistik.tu-dortmund.de (Uwe Ligges)
Date: Sat, 13 Nov 2010 17:49:08 +0100
Subject: [Rd] installing dependencies: binary vs source
In-Reply-To: <4CDC8CFF.6080303@fhcrc.org>
References: <4CDC8CFF.6080303@fhcrc.org>
Message-ID: <4CDEC184.6000607@statistik.tu-dortmund.de>



On 12.11.2010 01:40, Herv? Pag?s wrote:
> Hi,
>
> Installing from binaries on Windows:
>
>  > install.packages("multtest")
> Warning: dependency 'Biobase' is not available
> trying URL
> 'http://cran.fhcrc.org/bin/windows/contrib/2.12/multtest_2.6.0.zip'
> Content type 'application/zip' length 1645590 bytes (1.6 Mb)
> opened URL
> downloaded 1.6 Mb
>
> package 'multtest' successfully unpacked and MD5 sums checked
>
> The downloaded packages are in
>
> C:\Users\biocbuild2\AppData\Local\Temp\2\RtmpPzRqzb\downloaded_packages
>
> Note the warning that a dependency is missing. But still the package
> got installed even though it won't be loadable.
>
> Now installing from source on Windows:
>
>  > install.packages("multtest", type="source")
> Warning: dependency 'Biobase' is not available
> trying URL 'http://cran.fhcrc.org/src/contrib/multtest_2.6.0.tar.gz'
> Content type 'application/x-gzip' length 1457444 bytes (1.4 Mb)
> opened URL
> downloaded 1.4 Mb
>
> ERROR: dependency 'Biobase' is not available for package 'multtest'
> * removing 'D:/biocbld/bbs-2.7-bioc/R/library/multtest'
>
> The downloaded packages are in
>
> 'C:\Users\biocbuild2\AppData\Local\Temp\2\RtmpPzRqzb\downloaded_packages'
> Warning message:
> In install.packages("multtest", type = "source") :
> installation of package 'multtest' had non-zero exit status
>
> Note the warning *and* ERROR.
>
> Is this the intended behavior of install.packages() when installing
> from binaries?


Herv?,

yes, I think so. If you ask to install a package, it is installed unless 
it cannot be installed (as it was the case since R had to load Biobase 
which was unavailable).


Best,
Uwe



> Thanks,
> H.
>
> PS: Sorry I don't have access to an R-2.13 installation where I can
> test this at the moment.
>
>  > sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
>



[Rd] installing dependencies: binary vs source
Uwe Ligges