[BioC] problem while loading affycoretools

James W. MacDonald jmacdon at uw.edu
Mon Sep 16 19:11:14 CEST 2013


Hi Mayte,

I am unable to replicate your issue. I just installed R-3.0.1 on my 
MacOS X box, and then did the following:

source("http://www.bioconductor.org/biocLite.R")
biocLite()
biocLite("affycoretools")
library(affycoretools)
sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets methods
[8] base

other attached packages:
  [1] affycoretools_1.32.1 KEGG.db_2.9.1        GO.db_2.9.0
  [4] RSQLite_0.11.4       DBI_0.2-7            AnnotationDbi_1.22.6
  [7] affy_1.38.1          Biobase_2.20.1       BiocGenerics_0.6.0
[10] BiocInstaller_1.10.3

loaded via a namespace (and not attached):
  [1] AnnotationForge_1.2.2   BSgenome_1.28.0 Biostrings_2.28.0
  [4] Category_2.26.0         GOstats_2.26.0 GSEABase_1.22.0
  [7] GenomicFeatures_1.12.3  GenomicRanges_1.12.5 Hmisc_3.12-2
[10] IRanges_1.18.3          MASS_7.3-29 PFAM.db_2.9.0
[13] R.methodsS3_1.5.0       R.oo_1.15.1 R.utils_1.26.2
[16] R2HTML_2.2.1            RBGL_1.36.2 RColorBrewer_1.0-5
[19] RCurl_1.95-4.1          ReportingTools_2.0.1 Rsamtools_1.12.4
[22] VariantAnnotation_1.6.7 XML_3.95-0.2 affyio_1.28.0
[25] annaffy_1.32.0          annotate_1.38.0 biomaRt_2.16.0
[28] biovizBase_1.8.1        bit_1.1-10 bitops_1.0-6
[31] cluster_1.14.4          codetools_0.2-8 colorspace_1.2-2
[34] dichromat_2.0-0         digest_0.6.3 edgeR_3.2.4
[37] ff_2.2-11               foreach_1.4.1 gcrma_2.32.0
[40] gdata_2.13.2            genefilter_1.42.0 ggbio_1.8.5
[43] ggplot2_0.9.3.1         gplots_2.11.3 graph_1.38.3
[46] grid_3.0.1              gridExtra_0.9.1 gtable_0.1.2
[49] gtools_3.0.0            hwriter_1.3 iterators_1.0.6
[52] labeling_0.2            lattice_0.20-23 limma_3.16.7
[55] munsell_0.4.2           oligoClasses_1.22.0 plyr_1.8
[58] preprocessCore_1.22.0   proto_0.3-10 reshape2_1.2.2
[61] rpart_4.1-3             rtracklayer_1.20.4 scales_0.2.3
[64] splines_3.0.1           stats4_3.0.1 stringr_0.6.2
[67] survival_2.37-4         tools_3.0.1 xtable_1.7-1
[70] zlibbioc_1.6.0

As you can see, both bit and ff installed correctly.

Are you installing source or binary packages?

Best,

Jim



On 9/16/13 12:14 PM, Mayte Suarez-Farinas wrote:
> Dear James, Henrik and Steve
>
> I tried biocLite("ff") and got the msg: package ‘ff’ is not available (for R version 3.0.1)
> (see below). Then I went ahead and download the tar package form (http://cran.r-project.org/web/packages/ff/index.html) and used R CMD install to install it. However,
> while loading ff (library(ff)) it complains that the package bit was missing, biocLite gave me
> same error (package ‘bit’ is not available (for R version 3.0.1) ) and I could not instll via CMD install
> gave me the following error
>
> dhcp-129-85-243-253:Desktop mayte$ R CMD INSTALL bit_1.1-10.tar
> * installing to library ‘/Users/mayte/Library/R/3.0/library’
> * installing *source* package ‘bit’ ...
> ** package ‘bit’ successfully unpacked and MD5 sums checked
> ** libs
> sh: make: command not found
> ERROR: compilation failed for package ‘bit’
> * removing ‘/Users/mayte/Library/R/3.0/library/bit’
> dhcp-129-85-243-253:Desktop mayte$
>
> Please help out, life without affycoretools is very difficult ;-)
>
>
> From: James W. MacDonald [jmacdon at uw.edu]
> Sent: Monday, September 16, 2013 11:03 AM
> To: Mayte Suarez-Farinas
> Cc: bioconductor at r-project.org
> Subject: Re: [BioC] problem while loading affycoretools
>
> Hi Mayte,
>
> I have not seen this error in the past. Have you tried simply installing
> ff first?
>
> biocLite("ff")
> biocLite("affycoretools")
>
> Best,
>
> Jim
>
>
> On 9/15/2013 4:57 PM, Mayte Suarez-Farinas wrote:
>> I updated to the most recent R version. After this brand new installation, I get the following error while loading library affycoretools:
>>
>> library(affycoretools)
>> Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
>>     there is no package called ‘ff’
>> Error: package or namespace load failed for ‘affycoretools’
>>
>> After checking mailing list, I followed James advice (https://stat.ethz.ch/pipermail/bioconductor/2012-December/049895.html) and updated all packages
>> library(BiocInstaller)
>> biocLite(character(0))
>>
>> Additionally, I updated all R packages as well
>>
>> Still, the same problem arise. My R session info is bellow
>>
>>
>> R version 3.0.1 (2013-05-16)
>> Platform: x86_64-apple-darwin10.8.0 (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] parallel  stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] KEGG.db_2.9.1        GO.db_2.9.0          RSQLite_0.11.4       DBI_0.2-7
>> [5] AnnotationDbi_1.22.6 affy_1.38.1          Biobase_2.20.1       BiocGenerics_0.6.0
>> [9] BiocInstaller_1.10.3
>>
>> loaded via a namespace (and not attached):
>>    [1] affyio_1.28.0         annaffy_1.32.0        annotate_1.38.0
>>    [4] AnnotationForge_1.2.2 biomaRt_2.16.0        Biostrings_2.28.0
>>    [7] Category_2.26.0       gcrma_2.32.0          gdata_2.13.2
>> [10] genefilter_1.42.0     GenomicRanges_1.12.5  GOstats_2.26.0
>> [13] gplots_2.11.3         graph_1.38.3          grid_3.0.1
>> [16] GSEABase_1.22.0       gtools_3.0.0          IRanges_1.18.3
>> [19] lattice_0.20-23       limma_3.16.7          preprocessCore_1.22.0
>> [22] R2HTML_2.2.1          RBGL_1.36.2           RCurl_1.95-4.1
>> [25] splines_3.0.1         stats4_3.0.1          survival_2.37-4
>> [28] tools_3.0.1           XML_3.95-0.2          xtable_1.7-1
>> [31] zlibbioc_1.6.0
>>
>>
>>        [[alternative HTML version deleted]]
>>
>>
>>
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> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>



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