[BioC] Error loading charm

[Dan Tenenbaum]

[cc'ing package maintainer]

On Thu, May 3, 2012 at 5:48 AM, Benilton Carvalho
<beniltoncarvalho at gmail.com> wrote:
> I can't reproduce the issue... I just installed it (using both
> type='source' and type='mac.binary.leopard') and everything worked as
> expected...

I can't reproduce this either.

I suggest the following:

Start R with
R --vanilla

Update all installed packages with:
source("http://bioconductor.org/biocLite.R")
biocLite(character(), ask=FALSE)

Dan


>
>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> 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 datasets  utils     methods   base
>
> other attached packages:
>  [1] charm_2.2.0         genefilter_1.38.0   fields_6.6.3
>  [4] spam_0.28-0         SQN_1.0.4           nor1mix_1.1-3
>  [7] mclust_3.4.11       Biobase_2.16.0      BiocGenerics_0.2.0
> [10] BiocInstaller_1.4.4 RColorBrewer_1.0-5
>
> loaded via a namespace (and not attached):
>  [1] affxparser_1.28.0     affyio_1.24.0         annotate_1.34.0
>  [4] AnnotationDbi_1.18.0  Biostrings_2.24.1     bit_1.1-9
>  [7] BSgenome_1.24.0       codetools_0.2-8       DBI_0.2-5
> [10] ff_2.2-6              foreach_1.4.0         GenomicRanges_1.8.3
> [13] gtools_2.6.2          IRanges_1.14.2        iterators_1.0.6
> [16] limma_3.12.0          MASS_7.3-17           multtest_2.12.0
> [19] oligo_1.21.3          oligoClasses_1.18.0   parallel_2.15.0
> [22] preprocessCore_1.18.0 RSQLite_0.11.1        siggenes_1.30.0
> [25] splines_2.15.0        stats4_2.15.0         survival_2.36-12
> [28] sva_3.2.0             tools_2.15.0          xtable_1.7-0
> [31] zlibbioc_1.2.0
>
>
> On 3 May 2012 13:37, Francesco Mancuso <francesco.mancuso at crg.eu> wrote:
>> Hi!
>> with the usual
>>
>>     source("http://bioconductor.org/biocLite.R")
>>     biocLite("charm")
>>
>> Cheers,
>> Francesco
>>
>>
>> On 03/05/2012 14:33, Benilton Carvalho wrote:
>>
>> How did you install 'charm'?
>>
>>
>> On 3 May 2012 12:50, Francesco Mancuso <francesco.mancuso at crg.eu> wrote:
>>
>> Dear list,
>> I have the following error when calling the package "charm".
>>
>>  > library(charm)
>> Error in get(Info[i, 1], envir = env) :
>>   internal error -3 in R_decompress1
>> Error: package/namespace load failed for 'charm'
>>
>> Do you have any ideas of what does it mean?
>> Meny thanks in advance.
>>
>> Best,
>> Francesco
>>
>>
>>  > sessionInfo()
>> R version 2.15.0 (2012-03-30)
>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>
>> locale:
>> [1] C/en_US.UTF-8/C/C/C/C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>>  [1] bit_1.1-8           genefilter_1.38.0   RColorBrewer_1.0-5
>> fields_6.6.3        spam_0.28-0         SQN_1.0.4           nor1mix_1.1-3
>>  [8] mclust_3.4.11       Biobase_2.16.0      BiocGenerics_0.2.0
>> BiocInstaller_1.4.4
>>
>> loaded via a namespace (and not attached):
>>  [1] AnnotationDbi_1.18.0 DBI_0.2-5            IRanges_1.14.2
>> RSQLite_0.11.1       affxparser_1.28.0    affyio_1.24.0
>>  [7] annotate_1.34.0      splines_2.15.0       stats4_2.15.0
>> survival_2.36-14     tools_2.15.0         xtable_1.7-0
>> [13] zlibbioc_1.2.0
>> --
>>
>> *Francesco Mattia Mancuso*
>> Bioinformatician
>>
>> - Bioinformatics Core Facility
>> - Proteomics Core Facility
>>
>> CRG-Centre for Genomic Regulation (Room 439)
>> C/ Dr. Aiguader, 88 (Edif. PRBB)
>> 08003 Barcelona, Spain
>>
>> Mail: francesco.mancuso at crg.eu <mailto:francesco.mancuso at crg.eu>
>> Phone: +34 933160202
>> http://www.crg.es/bioinformatics_unit
>>
>>        [[alternative HTML version deleted]]
>>
>> _______________________________________________
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>>
>> .
>>
>>
>> --
>>
>> Francesco Mattia Mancuso
>> Bioinformatician
>>
>> - Bioinformatics Core Facility
>> - Proteomics Core Facility
>>
>> CRG-Centre for Genomic Regulation (Room 439)
>> C/ Dr. Aiguader, 88 (Edif. PRBB)
>> 08003 Barcelona, Spain
>>
>> Mail: francesco.mancuso at crg.eu
>> Phone: +34 933160202
>> http://www.crg.es/bioinformatics_unit
>
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