[BioC] Bioconductor affy package installation issues

Fri Feb 27 05:07:48 CET 2009

Dear Wolfgang and Martin,

Thank you very much for your suggestions.  Looks like my problem was 
entirely self-inflicted - I did not do a "make uninstall" when upgrading to 
R 2.8.1, which kept some old versions of bioconductor libraries.

A complete uninstall and a re-installation of R appears to have resolved all 
issues.

Thank you very much for your help!

Sincerely,

Boris Umylny

----- Original Message ----- 
From: "Martin Morgan" <mtmorgan at fhcrc.org>
To: "Wolfgang Huber" <huber at ebi.ac.uk>
Cc: "Boris Umylny" <umylny at apbri.org>; <bioconductor at stat.math.ethz.ch>
Sent: Friday, February 27, 2009 1:03 AM
Subject: Re: [BioC] Bioconductor affy package installation issues

Wolfgang Huber <huber at ebi.ac.uk> writes:

> 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.

Since bioconductor packages are versioned in synch with R, it is
usually sufficient to follow the instructions at

  http://bioconductor.org/docs/install/

and, in a new R session

> source("http://bioconductor.org/biocLite.R")
> update.packages(repos=biocinstallRepos(), ask=FALSE)

(or ask=TRUE if you'd like more interactivity with your update).

This strategy might not be sufficient if you had updated your
operating system rather than R, so that new system libraries need to
be linked.

Another situation where it might not be sufficient is if there had
been a change in R that broke a package, and the package had not been
updated -- the package would fail when used, and there would be no
correction available; the behavior with 'wipe the library' would often
be the same, i.e., the incompatibility would not be detected until the
code was actually used after installation.

Martin

> 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]]
>>>
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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