[BioC] error while loading the genefilter package [R 2.8.1. on Mac OSX 10.5.6]
Richard Pearson
richard.pearson at well.ox.ac.uk
Wed Apr 15 19:04:54 CEST 2009
Patrick
I think I've got a similar problem with a collaborator who is also on OS X
10.5.6 and R 2.8.1, but here the problem is with the affy package. For some
reason, it appears that biocLite is installing the OS X 10.4 version of the
binary (from http://bioconductor.org/packages/2.3/bioc/bin/macosx/universal)
rather then the 10.5 version (from
http://bioconductor.org/packages/2.3/bioc/bin/macosx/leopard). Could this be a
bug in biocLite?
Here is the output from trying to install and load "affy", and the sessionInfo()
> 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/bin/macosx/universal/contrib/2.8/affy_1.20.2.tgz'
Content type 'application/x-gzip' length 1439037 bytes (1.4 Mb)
opened URL
==================================================
downloaded 1.4 Mb
The downloaded packages are in
/var/folders/B7/B77yjISEE1iKVBJQ80Q+lk+++TI/-Tmp-//Rtmp0yyhTV/downloaded_packages
> library("affy")
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)'.
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library
'/Library/Frameworks/R.framework/Resources/library/preprocessCore/libs/i386/preprocessCore.so':
dlopen(/Library/Frameworks/R.framework/Resources/library/preprocessCore/libs/i386/preprocessCore.so,
6): Library not loaded: /usr/local/lib/libgfortran.2.dylib
Referenced from:
/Library/Frameworks/R.framework/Resources/library/preprocessCore/libs/i386/preprocessCore.so
Reason: image not found
Error: package/namespace load failed for 'affy'
>sessionInfo()
R version 2.8.1 (2008-12-22)
i386-apple-darwin8.11.1
locale:
en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] tools stats graphics grDevices utils datasets methods base
other attached packages:
[1] Biobase_2.2.2
loaded via a namespace (and not attached):
[1] affyio_1.10.1
Cheers
Richard
Massimo Pinto wrote:
> Hi Patrick, thank you for your assistance.
> Here is my SessionInfo()
>
>> sessionInfo()
> R version 2.8.1 (2008-12-22)
> i386-apple-darwin8.11.1
>
> locale:
> C
>
> attached base packages:
> [1] splines tools stats graphics grDevices utils
> [7] datasets methods base
>
> other attached packages:
> [1] survival_2.34-1 Biobase_2.2.2
>
> loaded via a namespace (and not attached):
> [1] AnnotationDbi_1.4.3 DBI_0.2-4 RSQLite_0.7-1
> [4] annotate_1.20.1
>
> ====
>
> If I install genefilter from BioC, right from the R console, I am getting
> the same results as I indicated in my earlier message. Perhaps you mean that
> I should download the sources and re-compile? Mmm I used to do these things
> in Linux, I need to take some dust off my neurons if I need to get this done
> on a Mac.
>
> Massimo
>
>
>
> On Wed, Apr 15, 2009 at 6:27 PM, Patrick Aboyoun <paboyoun at fhcrc.org> wrote:
>
>> Massimo,
>> The problem is in the version of the genefilter Mac OS X 10.5 (Leopard)
>> binary package you are using. I just downloaded genefilter version 1.22 for
>> BioC 2.3 from bioconductor.org and don't see the dynamic linking to
>> libgfortran that is suggested by your error message:
>>
>> sandbox$ otool -L genefilter/libs/i386/genefilter.so
>> genefilter/libs/i386/genefilter.so:
>> genefilter.so (compatibility version 0.0.0, current version 0.0.0)
>> /Library/Frameworks/R.framework/Versions/2.8/Resources/lib/libR.dylib
>> (compatibility version 2.8.0, current version 2.8.0)
>>
>> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
>> (compatibility version 150.0.0, current version 476.15.0)
>> /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version
>> 7.4.0)
>> /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version
>> 1.0.0)
>> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
>> 111.1.1)
>>
>> Try to reinstall genefilter using biocLite("genefilter") and let me know if
>> the problem persists. Perhaps it is with a different library. Include your
>> sessionInfo() in your response so I can help troubleshoot any problems that
>> arise.
>>
>>
>> Patrick
>>
>>
>>
>> Massimo Pinto wrote:
>>
>>> Greetings BioC list readers,
>>>
>>> on a Mac OSX 10.5.6 with R 2.8.1 I have successfully installed a series of
>>> packages by typing the following code on the R Console.
>>>
>>>
>>>
>>>> source("http://bioconductor.org/biocLite.R")
>>>> biocLite()
>>>>
>>>>
>>> [...]
>>>
>>> however, this is what I am getting when I try to load genefilter, which is
>>> required by the package Agi4x44PreProcess
>>>
>>>
>>>
>>>> library(genefilter)
>>>>
>>>>
>>> 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: survival
>>> Loading required package: splines
>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>> unable to load shared library
>>>
>>> '/Library/Frameworks/R.framework/Resources/library/genefilter/libs/i386/genefilter.so':
>>>
>>> dlopen(/Library/Frameworks/R.framework/Resources/library/genefilter/libs/i386/genefilter.so,
>>> 6): Library not loaded: /usr/local/lib/libgfortran.2.dylib
>>> Referenced from:
>>>
>>> /Library/Frameworks/R.framework/Resources/library/genefilter/libs/i386/genefilter.so
>>> Reason: image not found
>>> Error: package/namespace load failed for 'genefilter'
>>>
>>> There is no /Library/Frameworks/ directory on my disk. Looks like I have
>>> got
>>> a messy installation. Does this look familiar to any of you?
>>> Yours,
>>> Massimo
>>>
>>>
>>>
>>
>
>
--
Richard D Pearson richard.pearson at well.ox.ac.uk
Wellcome Trust Centre for Human Genetics http://www.well.ox.ac.uk/~rpearson
University of Oxford Tel: +44 (0)1865 287575
Roosevelt Drive Mob: +44 (0)7971 221181
Oxford OX3 7BN, UK Fax: +44 (0)1865 287664
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