[BioC] Bioconductor affy package installation issues

[Wolfgang Huber]

Dear Boris,

when you are recompiling R, the correct procedure is to wipe out all
installed add-on packages (in your case, they are in
/usr/local/lib64/R/library), in particular "preprocessCore", and to
re-install them using the new R. If you are not doing that, you risk
version incompatibilities both on the binary and the R level.

Also, there is no reason that R or its add-on packages should be
installed by "root". I think it is good practice to do this with a user
account with more restricted rights (and it can still be set up such
that every user on the system can run R and load the packages)

Best wishes
 Wolfgang

------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber


26/02/2009 06:54 Boris Umylny scripsit
> 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]]
>>