[BioC] problem while loading affycoretools

[Dan Tenenbaum]

----- Original Message -----
> From: "Mayte Suarez-Farinas" <farinam at mail.rockefeller.edu>
> To: "James W. MacDonald" <jmacdon at uw.edu>
> Cc: "Steve Lianoglou" <lianoglou.steve at gene.com>, bioconductor at r-project.org
> Sent: Monday, September 16, 2013 9:14:00 AM
> Subject: Re: [BioC] problem while loading affycoretools
> 
> 
> 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


You downloaded the source tarball for bit (.tar.gz); you wanted the Mac binary (.tgz).

As for the problem with biocLite("bit") I'm not sure--are you behind a proxy or firewall?
What is the output of the following:

library(BiocInstaller)
biocinstallRepos()

?

Dan


> 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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