[BioC] Rsamtools installation

[James W. MacDonald]

Hi John,

On 11/8/2011 9:33 AM, John Coulthard wrote:
> Hi
>
> I'm trying to install Rsamtools and getting errors!  I've tried...
>       install.packages("/home/ann/downloads/Rsamtools_1.6.0.tar.gz")
> and
>       biocLite("Rsamtools")
> (see below)
>
>
> Why doesn't  biocLite() install the current version?
> I'm almost sure the dependencies are all up-to-date using  install.packages().
> So if it's not an out of date dependent what could the problem be?
> If is it an out of date dependent how do I get R to tell me which one?

You appear to be going rogue here. You should not be using 
install.packages() at all, and should not be using an outdated version 
of biocLite().

You want

source("http://www.bioconductor.org/biocLite.R")

which will install the BiocInstaller package (and load it for you this time)

then in future, you should

library(BiocInstaller)
biocLite("Rsamtools")

which will

 > biocLite("Rsamtools")
BioC_mirror: 'http://www.bioconductor.org'
Using R version 2.14, BiocInstaller version 1.2.0.
Installing package(s) 'Rsamtools'
<snip>
trying URL 
'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/Rsamtools_1.6.0.tar.gz'
Content type 'application/x-gzip' length 2088510 bytes (2.0 Mb)


Note the message I get compared to what you got.

Best,

Jim



>
> Thanks
> John
>
>
>> install.packages("/home/ann/downloads/Rsamtools_1.6.0.tar.gz")
> Installing package(s) into ‘/usr/local/lib/R/site-library’
> (as ‘lib’ is unspecified)
> inferring 'repos = NULL' from the file name
> * installing *source* package ‘Rsamtools’ ...
> ** libs
> <snip>
> ** R
> ** inst
> ** preparing package for lazy loading
> Error : class "Sequence" is not exported by 'namespace:IRanges'
> ERROR: lazy loading failed for package ‘Rsamtools’
> * removing ‘/usr/local/lib/R/site-library/Rsamtools’
> Warning message:
> In install.packages("/home/ann/downloads/Rsamtools_1.6.0.tar.gz") :
>    installation of package ‘/home/ann/downloads/Rsamtools_1.6.0.tar.gz’ had non-zero exit status
>
>
>>   biocLite("Rsamtools")
> Using R version 2.14.0, biocinstall version 2.7.7.
> Installing Bioconductor version 2.7 packages:
> [1] "Rsamtools"
> Please wait...
>
> Installing package(s) into ‘/usr/local/lib/R/site-library’
> (as ‘lib’ is unspecified)
> trying URL 'http://bioconductor.org/packages/2.7/bioc/src/contrib/Rsamtools_1.2.3.tar.gz'
> Content type 'application/x-gzip' length 1618555 bytes (1.5 Mb)
> opened URL
> <snip>
> ** R
> ** inst
> ** preparing package for lazy loading
> Error : object ‘normalizePath’ is not exported by 'namespace:utils'
> ERROR: lazy loading failed for package ‘Rsamtools’
> * removing ‘/usr/local/lib/R/site-library/Rsamtools’
>
> The downloaded packages are in
>      ‘/tmp/RtmpkLT1S0/downloaded_packages’
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, ...) :
>    installation of package ‘Rsamtools’ had non-zero exit status
>
>
> Many thanks
> John
>
>
>   		 	   		
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>
>
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826

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