[BioC] problem while loading affycoretools

[Dan Tenenbaum]

----- Original Message -----
> From: "Mayte Suarez-Farinas" <farinam at mail.rockefeller.edu>
> To: "Dan Tenenbaum" <dtenenba at fhcrc.org>
> Cc: "Mayte Suarez-Farinas" <farinam at mail.rockefeller.edu>, "Steve Lianoglou" <lianoglou.steve at gene.com>,
> "<bioconductor at r-project.org>" <bioconductor at r-project.org>, "James W. MacDonald" <jmacdon at uw.edu>
> Sent: Monday, September 16, 2013 10:50:08 AM
> Subject: Re: [BioC] problem while loading affycoretools
> 
> 
> 
> Hi James and Dan
> 
> 
> I installed R from scratch and then run the following two lines:
> 
> 
> biocLite() (success)
> biocLite("affycoretools")
> 
> which, after installing several packages gave me the "error: package
> ‘AnnotationDbi’ could not be loaded" (see ALL outputs below)'
> 
> 
> Dan, here is the output of biocinstallRepos.
> librarybiocInstall()
> biocinstallRepos()
> 
> BioCsoft
> " http://bioconductor.org/packages/2.12/bioc "
> BioCann
> " http://bioconductor.org/packages/2.12/data/annotation "
> BioCexp
> " http://bioconductor.org/packages/2.12/data/experiment "
> BioCextra
> " http://bioconductor.org/packages/2.12/extra "
> CRAN
> " http://cran.opensourceresources.org "
> 

It appears that the CRAN mirror you are using is not working properly.
Try picking a mirror from this list:
http://cran.r-project.org/mirrors.html

You can change mirrors with the chooseCRANmirror() function.
Dan




> 
> 
> 
> ALL OUTPUTS:
> 
> 
> 
> 
> source(" http://bioconductor.org/biocLite.R ")
> Installing package into ‘/Users/mayte/Library/R/3.0/library’
> (as ‘lib’ is unspecified)
> trying URL '
> http://www.bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/BiocInstaller_1.10.3.tgz'
> Content type 'application/x-gzip' length 46533 bytes (45 Kb)
> opened URL
> ==================================================
> downloaded 45 Kb
> 
> 
> 
> 
> The downloaded binary packages are in
> /var/folders/r3/tlsb98mn33b3tl1wjd87hwch0000gn/T//RtmpARSLz6/downloaded_packages
> Bioconductor version 2.12 (BiocInstaller 1.10.3), ?biocLite for help
> > biocLite()
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version
> 3.0.1.
> Installing package(s) 'Biobase' 'IRanges' 'AnnotationDbi'
> Warning: unable to access index for repository
> http://cran.opensourceresources.org/bin/macosx/contrib/3.0
> Warning: dependencies ‘DBI’, ‘RSQLite’ are not available
> also installing the dependency ‘BiocGenerics’
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/BiocGenerics_0.6.0.tgz'
> Content type 'application/x-gzip' length 333465 bytes (325 Kb)
> opened URL
> ==================================================
> downloaded 325 Kb
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Biobase_2.20.1.tgz'
> Content type 'application/x-gzip' length 2354463 bytes (2.2 Mb)
> opened URL
> ==================================================
> downloaded 2.2 Mb
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/IRanges_1.18.3.tgz'
> Content type 'application/x-gzip' length 1978262 bytes (1.9 Mb)
> opened URL
> ==================================================
> downloaded 1.9 Mb
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/AnnotationDbi_1.22.6.tgz'
> Content type 'application/x-gzip' length 4066815 bytes (3.9 Mb)
> opened URL
> ==================================================
> downloaded 3.9 Mb
> 
> 
> 
> 
> The downloaded binary packages are in
> /var/folders/r3/tlsb98mn33b3tl1wjd87hwch0000gn/T//RtmpARSLz6/downloaded_packages
> Warning: unable to access index for repository
> http://cran.opensourceresources.org/bin/macosx/contrib/3.0
> > biocLite("affycoretools")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version
> 3.0.1.
> Installing package(s) 'affycoretools'
> Warning: unable to access index for repository
> http://cran.opensourceresources.org/bin/macosx/contrib/3.0
> Warning: dependencies ‘xtable’, ‘gplots’, ‘R2HTML’, ‘hwriter’, ‘XML’,
> ‘RCurl’, ‘DBI’, ‘foreach’, ‘R.utils’, ‘RSQLite’, ‘reshape2’,
> ‘gtable’, ‘gridExtra’, ‘scales’, ‘Hmisc’, ‘RColorBrewer’,
> ‘dichromat’, ‘bitops’ are not available
> also installing the dependencies ‘org.Hs.eg.db’, ‘biovizBase’,
> ‘GenomicFeatures’, ‘Rsamtools’, ‘BSgenome’, ‘VariantAnnotation’,
> ‘rtracklayer’, ‘affyio’, ‘preprocessCore’, ‘zlibbioc’, ‘Category’,
> ‘graph’, ‘RBGL’, ‘AnnotationForge’, ‘Biostrings’, ‘GenomicRanges’,
> ‘edgeR’, ‘PFAM.db’, ‘GSEABase’, ‘ggbio’, ‘affy’, ‘GO.db’, ‘KEGG.db’,
> ‘biomaRt’, ‘limma’, ‘GOstats’, ‘annotate’, ‘annaffy’, ‘gcrma’,
> ‘oligoClasses’, ‘ReportingTools’
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/data/annotation/bin/macosx/contrib/3.0/org.Hs.eg.db_2.9.0.tgz'
> Content type 'application/x-gzip' length 53095874 bytes (50.6 Mb)
> opened URL
> ==================================================
> downloaded 50.6 Mb
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/biovizBase_1.8.1.tgz'
> Content type 'application/x-gzip' length 1136533 bytes (1.1 Mb)
> opened URL
> ==================================================
> downloaded 1.1 Mb
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/GenomicFeatures_1.12.3.tgz'
> Content type 'application/x-gzip' length 971035 bytes (948 Kb)
> opened URL
> ==================================================
> downloaded 948 Kb
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Rsamtools_1.12.4.tgz'
> Content type 'application/x-gzip' length 3768247 bytes (3.6 Mb)
> opened URL
> ==================================================
> downloaded 3.6 Mb
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/BSgenome_1.28.0.tgz'
> Content type 'application/x-gzip' length 746888 bytes (729 Kb)
> opened URL
> ==================================================
> downloaded 729 Kb
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/VariantAnnotation_1.6.7.tgz'
> Content type 'application/x-gzip' length 1689203 bytes (1.6 Mb)
> opened URL
> ==================================================
> downloaded 1.6 Mb
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/rtracklayer_1.20.4.tgz'
> Content type 'application/x-gzip' length 1861493 bytes (1.8 Mb)
> opened URL
> ==================================================
> downloaded 1.8 Mb
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/affyio_1.28.0.tgz'
> Content type 'application/x-gzip' length 94024 bytes (91 Kb)
> opened URL
> ==================================================
> downloaded 91 Kb
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/preprocessCore_1.22.0.tgz'
> Content type 'application/x-gzip' length 128027 bytes (125 Kb)
> opened URL
> ==================================================
> downloaded 125 Kb
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/zlibbioc_1.6.0.tgz'
> Content type 'application/x-gzip' length 124184 bytes (121 Kb)
> opened URL
> ==================================================
> downloaded 121 Kb
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Category_2.26.0.tgz'
> Content type 'application/x-gzip' length 933299 bytes (911 Kb)
> opened URL
> ==================================================
> downloaded 911 Kb
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/graph_1.38.3.tgz'
> Content type 'application/x-gzip' length 1327243 bytes (1.3 Mb)
> opened URL
> ==================================================
> downloaded 1.3 Mb
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/RBGL_1.36.2.tgz'
> Content type 'application/x-gzip' length 911905 bytes (890 Kb)
> opened URL
> ==================================================
> downloaded 890 Kb
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/AnnotationForge_1.2.2.tgz'
> Content type 'application/x-gzip' length 4149568 bytes (4.0 Mb)
> opened URL
> ==================================================
> downloaded 4.0 Mb
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Biostrings_2.28.0.tgz'
> Content type 'application/x-gzip' length 2215378 bytes (2.1 Mb)
> opened URL
> ==================================================
> downloaded 2.1 Mb
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/GenomicRanges_1.12.5.tgz'
> Content type 'application/x-gzip' length 3293184 bytes (3.1 Mb)
> opened URL
> ==================================================
> downloaded 3.1 Mb
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/edgeR_3.2.4.tgz'
> Content type 'application/x-gzip' length 1470863 bytes (1.4 Mb)
> opened URL
> ==================================================
> downloaded 1.4 Mb
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/data/annotation/bin/macosx/contrib/3.0/PFAM.db_2.9.0.tgz'
> Content type 'application/x-gzip' length 2325707 bytes (2.2 Mb)
> opened URL
> ==================================================
> downloaded 2.2 Mb
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/GSEABase_1.22.0.tgz'
> Content type 'application/x-gzip' length 606089 bytes (591 Kb)
> opened URL
> ==================================================
> downloaded 591 Kb
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/ggbio_1.8.5.tgz'
> Content type 'application/x-gzip' length 2272353 bytes (2.2 Mb)
> opened URL
> ==================================================
> downloaded 2.2 Mb
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/affy_1.38.1.tgz'
> Content type 'application/x-gzip' length 1458286 bytes (1.4 Mb)
> opened URL
> ==================================================
> downloaded 1.4 Mb
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/data/annotation/bin/macosx/contrib/3.0/GO.db_2.9.0.tgz'
> Content type 'application/x-gzip' length 25061115 bytes (23.9 Mb)
> opened URL
> ==================================================
> downloaded 23.9 Mb
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/data/annotation/bin/macosx/contrib/3.0/KEGG.db_2.9.1.tgz'
> Content type 'application/x-gzip' length 2032486 bytes (1.9 Mb)
> opened URL
> ==================================================
> downloaded 1.9 Mb
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/biomaRt_2.16.0.tgz'
> Content type 'application/x-gzip' length 365452 bytes (356 Kb)
> opened URL
> ==================================================
> downloaded 356 Kb
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/limma_3.16.7.tgz'
> Content type 'application/x-gzip' length 1568068 bytes (1.5 Mb)
> opened URL
> ==================================================
> downloaded 1.5 Mb
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/GOstats_2.26.0.tgz'
> Content type 'application/x-gzip' length 1725303 bytes (1.6 Mb)
> opened URL
> ==================================================
> downloaded 1.6 Mb
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/annotate_1.38.0.tgz'
> Content type 'application/x-gzip' length 1971349 bytes (1.9 Mb)
> opened URL
> ==================================================
> downloaded 1.9 Mb
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/annaffy_1.32.0.tgz'
> Content type 'application/x-gzip' length 380113 bytes (371 Kb)
> opened URL
> ==================================================
> downloaded 371 Kb
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/gcrma_2.32.0.tgz'
> Content type 'application/x-gzip' length 240351 bytes (234 Kb)
> opened URL
> ==================================================
> downloaded 234 Kb
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/oligoClasses_1.22.0.tgz'
> Content type 'application/x-gzip' length 872393 bytes (851 Kb)
> opened URL
> ==================================================
> downloaded 851 Kb
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/ReportingTools_2.0.1.tgz'
> Content type 'application/x-gzip' length 2063622 bytes (2.0 Mb)
> opened URL
> ==================================================
> downloaded 2.0 Mb
> 
> 
> trying URL '
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/affycoretools_1.32.1.tgz'
> Content type 'application/x-gzip' length 7077475 bytes (6.7 Mb)
> opened URL
> ==================================================
> downloaded 6.7 Mb
> 
> 
> 
> 
> The downloaded binary packages are in
> /var/folders/r3/tlsb98mn33b3tl1wjd87hwch0000gn/T//RtmpARSLz6/downloaded_packages
> Warning: unable to access index for repository
> http://cran.opensourceresources.org/bin/macosx/contrib/3.0
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> Mayte Suarez-Farinas
> Research Assistant Professor
> Laboratory of Investigative Dermatology
> Biostatistician, Center for Clinical and Translational Science
> The Rockefeller University
> 1230 York Ave, Box 178
> New York, NY 10065
> Phone: +1(212) 327-8213
> Fax: +1(212) 327-8232
> 
> 
> 
> 
> 
> On Sep 16, 2013, at 1:36 PM, Dan Tenenbaum wrote:
> 
> 
> 
> 
> 
> ----- 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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> 
> 
> _______________________________________________
> 
> 
> 
> 
> 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
> 
> 
> 
> 
> 
> --
> 
> 
> James W. MacDonald, M.S.
> 
> 
> Biostatistician
> 
> 
> University of Washington
> 
> 
> Environmental and Occupational Health Sciences
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