[BioC] Bioc packages not working with R2.15.2?

Fri Nov 16 17:39:51 CET 2012

On Fri, Nov 16, 2012 at 8:28 AM, Benilton Carvalho
<beniltoncarvalho at gmail.com> wrote:
> Looks like there is some mix & matching going on? (mentioning this because
> it seems intriguing - for me - the fact that you're running R-2.15.2, but
> the error also refers to R.framework/Versions/2.13)
>
> Note that the package that is failing is 'bit' (which is not a BioC
> package), so reinstall it (the failure is because R cannot find the 64-bit
> image of that package) and its friends (the ff package). Also allow
> BiocInstaller to update your existing packages. Although they're not a BioC
> packages, you can use biocLite() for the task:
>
>> biocLite(c('bit', 'ff'))
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
> Installing package(s) 'bit' 'ff'
> trying URL '
> http://cran.fhcrc.org/bin/macosx/leopard/contrib/2.15/bit_1.1-9.tgz'
> Content type 'application/x-gzip' length 223228 bytes (217 Kb)
> opened URL
> ==================================================
> downloaded 217 Kb
>
> trying URL '
> http://cran.fhcrc.org/bin/macosx/leopard/contrib/2.15/ff_2.2-10.tgz'
> Content type 'application/x-gzip' length 1629830 bytes (1.6 Mb)
> opened URL
> ==================================================
> downloaded 1.6 Mb
>
>
> Regarding the error with the installation of RSQLite, I can't reproduce the
> issue:
>

This is probably because your mirror is not up to date. Try setting it
to the master as follows:
options("BioC_mirror" = "http://www.bioconductor.org")
Then:
source("http://bioconductor.org/biocLite.R")
biocLite("RSQLite")

Dan

>> biocLite("RSQLite")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
> Installing package(s) 'RSQLite'
> trying URL '
> http://cran.fhcrc.org/bin/macosx/leopard/contrib/2.15/RSQLite_0.11.2.tgz'
> Content type 'application/x-gzip' length 2219524 bytes (2.1 Mb)
> opened URL
> ==================================================
> downloaded 2.1 Mb
>> sessionInfo()
> R version 2.15.2 RC (2012-10-25 r61014)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] BiocInstaller_1.8.3
>
> loaded via a namespace (and not attached):
> [1] tools_2.15.2
>
>
>
> On 16 November 2012 15:12, YBao <yb8d at virginia.edu> wrote:
>
>> Hi All,
>>
>> I recently updated my R to 2.15.2 and reloaded the bioc packages. Then I
>> started to have troubles making use of a number of packages, not the least
>> with OLIGO which I have been using frequently before this updating. Can
>> someone in the know lend a helping hand on this. Below is the error message
>>
>> > library(oligo)
>> Loading required package: oligoClasses
>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>   unable to load shared object
>> '/Users/yb8d/Library/R/2.15/library/bit/libs/x86_64/bit.so':
>>   dlopen(/Users/yb8d/Library/R/2.15/library/bit/libs/x86_64/bit.so, 6):
>> Library not loaded:
>> /Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libR.dylib
>>   Referenced from:
>> /Users/yb8d/Library/R/2.15/library/bit/libs/x86_64/bit.so
>>   Reason: image not found
>> Error: package ‘oligoClasses’ could not be loaded
>>
>> Then when I tried to load RSQLite I got this error:
>> > biocLite("RSQLite")
>> BioC_mirror: http://bioconductor.org
>> Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
>> Installing package(s) 'RSQLite'
>> Warning: unable to access index for repository
>> http://software.rc.fas.harvard.edu/mirrors/R/src/contrib
>> Warning: unable to access index for repository
>>
>> http://software.rc.fas.harvard.edu/mirrors/R/bin/macosx/leopard/contrib/2.15
>> Warning: unable to access index for repository
>>
>> http://software.rc.fas.harvard.edu/mirrors/R/bin/macosx/leopard/contrib/2.15
>> Warning message:
>> package ‘RSQLite’ is not available (for R version 2.15.2)
>>
>> And my sessionInfo:
>> R version 2.15.2 (2012-10-26)
>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>>  [1] BiocInstaller_1.8.3   ALL_1.4.13            RColorBrewer_1.0-2
>>  lattice_0.20-10       limma_3.14.1          affyPLM_1.34.0
>>  preprocessCore_1.20.0
>>  [8] gcrma_2.30.0          affydata_1.11.17      affy_1.36.0
>> Biobase_2.18.0        BiocGenerics_0.4.0    R.utils_1.7.5
>> R.oo_1.8.0
>> [15] R.methodsS3_1.2.1
>>
>> loaded via a namespace (and not attached):
>>  [1] affyio_1.26.0        Biostrings_2.26.2    DBI_0.2-5
>>  GenomicRanges_1.10.5 grid_2.15.2          IRanges_1.16.4
>> parallel_2.15.2
>>  [8] splines_2.15.2       stats4_2.15.2        tools_2.15.2
>> xtable_1.5-6         zlibbioc_1.4.0
>>
>> Best,
>>
>> Yongde
>>
>>
>> --
>> Yongde Bao
>> Dept. of Microbiology, Immunology,
>>              and Cancer Biology
>> UVA
>>
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>>
>>
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>
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