[BioC] problem while loading affycoretools

[Mayte Suarez-Farinas]

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