[BioC] Error loading charm
Benilton Carvalho
beniltoncarvalho at gmail.com
Fri May 4 10:28:25 CEST 2012
This suggests you're installing from the source... in which case, you
may benefit from using something along the lines of:
biocLite('Pkg Name', type='source', INSTALL_opts="--merge-multiarch")
this should download the source and install it for both architectures.
b
On 4 May 2012 09:17, Francesco Mancuso <francesco.mancuso at crg.eu> wrote:
> Hi all!
> I think I solved the problem reinstalling the package "bit".
>
> Since the last R version, I have always problem installing packages from
> CRAN using GUI of R 64bit. The installation goes well but then it's like if
> the 32bit version of the package is missing.
> Usually the error is that a library is missing and not the strange one I
> had.
>
> Many thanks for the support.
> Best,
> Francesco
>
>
> On 03/05/2012 21:11, Harris A. Jaffee wrote:
>
> A shot in the dark here.
>
> What happens if you do
>
> library(charm)
>
> immediately after starting R, with nothing else loaded?
>
> Do some packages successfully load, like perhaps
>
> Loading required package: Biobase
> Loading required package: BiocGenerics
> ...
>
> If so, what are they? Or does it fail immediately?
>
> It would be good to know the exact point of failure.
>
> On May 3, 2012, at 2:16 PM, Dan Tenenbaum wrote:
>
> [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]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> .
>
>
> --
>
> 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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> .
>
>
> --
>
> 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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