[BioC] Bioconductor affy package installation issues

[Boris Umylny]

Robert,

Thank you very much for your reply.

I tried to run biocLite(), however that failed (messages below the 
signature).

I then tried to load affy using biocLite("affy"), that failed again with the 
same messages as last time.

Should I reinstall R?

Thank you in advance for your help.


Sincerely,


Boris Umylny

............
** R
** inst
** preparing package for lazy loading
Error: package 'affy' required by 'affyPLM' could not be found
Execution halted
ERROR: lazy loading failed for package 'affyPLM'
** Removing '/usr/local/lib64/R/library/affyPLM'
* Installing *source* package 'affyQCReport' ...
** R
** inst
** preparing package for lazy loading
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: affy
Warning in library(pkg, character.only = TRUE, logical.return = TRUE, 
lib.loc = lib.loc) :
  there is no package called 'affy'
Error: package 'affy' could not be loaded
Execution halted
ERROR: lazy loading failed for package 'affyQCReport'
** Removing '/usr/local/lib64/R/library/affyQCReport'

The downloaded packages are in
        /tmp/RtmpGwRvXr/downloaded_packages
Updating HTML index of packages in '.Library'
There were 12 warnings (use warnings() to see them)



----- Original Message ----- 
From: "Robert Gentleman" <rgentlem at fhcrc.org>
To: "Boris Umylny" <umylny at apbri.org>
Cc: <bioconductor at stat.math.ethz.ch>
Sent: Thursday, February 26, 2009 2:37 PM
Subject: Re: [BioC] Bioconductor affy package installation issues


Hi Boris,
  It looks like you have an outdated preprocessCore package, I would
suggest that you do a complete reinstall not just one package
 eg biocLite()

best wishes
  Robert


On Wed, Feb 25, 2009 at 9:16 PM, Boris Umylny <umylny at apbri.org> wrote:
> Dear All:
>
> I have upgraded our R to 2.8.1 version and attempted to reinstall the affy 
> package from bioconductor. The installation attempt failed (the R output 
> is below my signature). During the installation I was running R as root.
>
> Any suggestion you may have about this issue would be greatly appreciated. 
> Thank you in advance for your help.
>
>
> Sincerely,
>
>
> Boris Umylny
>
> The R session log:
>
>> source("http://bioconductor.org/biocLite.R")
>> biocLite("affy")
> Running biocinstall version 2.3.10 with R version 2.8.1
> Your version of R requires version 2.3 of Bioconductor.
> trying URL 
> 'http://bioconductor.org/packages/2.3/bioc/src/contrib/affy_1.20.2.tar.gz'
> Content type 'application/x-gzip' length 1136034 bytes (1.1 Mb)
> opened URL
> ==================================================
> downloaded 1.1 Mb
>
> * Installing *source* package 'affy' ...
> creating cache ./config.cache
> checking how to run the C preprocessor... cc -E
> checking for main in -lz... yes
> checking for zlib.h... yes
> checking if zlib version >= 1.1.3... yes
> updating cache ./config.cache
> creating ./config.status
> creating src/Makevars
> ** libs
> gcc -std=gnu99 -I/usr/local/lib64/R/include -DHAVE_ZLIB=1 -I/usr/local/include 
>  -I"/usr/local/lib64/R/library/preprocessCore/include" -fpic -g -O2 -c 
> chipbackground.c -o chipbackground.o
> gcc -std=gnu99 -I/usr/local/lib64/R/include -DHAVE_ZLIB=1 -I/usr/local/include 
>  -I"/usr/local/lib64/R/library/preprocessCore/include" -fpic -g -O2 -c 
> getall_locations.c -o getall_locations.o
> gcc -std=gnu99 -I/usr/local/lib64/R/include -DHAVE_ZLIB=1 -I/usr/local/include 
>  -I"/usr/local/lib64/R/library/preprocessCore/include" -fpic -g -O2 -c 
> mas5calls.c -o mas5calls.o
> gcc -std=gnu99 -I/usr/local/lib64/R/include -DHAVE_ZLIB=1 -I/usr/local/include 
>  -I"/usr/local/lib64/R/library/preprocessCore/include" -fpic -g -O2 -c 
> rma2.c -o rma2.o
> rma2.c:123:31: error: R_subColSummarize.h: No such file or directory
> rma2.c:124:37: error: R_subColSummarize_stubs.c: No such file or directory
> rma2.c: In function âdo_RMA2â:
> rma2.c:133: warning: implicit declaration of function 
> âR_subColSummarize_medianpolish_logâ
> rma2.c:133: warning: assignment makes pointer from integer without a cast
> make: *** [rma2.o] Error 1
> chmod: cannot access `/usr/local/lib64/R/library/affy/libs/*': No such 
> file or directory
> ERROR: compilation failed for package 'affy'
> ** Removing '/usr/local/lib64/R/library/affy'
>
> The downloaded packages are in
> /tmp/Rtmpgb8Bd0/downloaded_packages
> Updating HTML index of packages in '.Library'
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, dependencies = 
> dependencies, :
> installation of package 'affy' had non-zero exit status
>> sessionInfo()
> R version 2.8.1 (2008-12-22)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> loaded via a namespace (and not attached):
> [1] tools_2.8.1
>>
>
> [[alternative HTML version deleted]]
>
>
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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org