[BioC] problem while loading affycoretools
Dan Tenenbaum
dtenenba at fhcrc.org
Mon Sep 16 20:53:17 CEST 2013
----- 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" <bioconductor at r-project.org>, "James W. MacDonald" <jmacdon at uw.edu>
> Sent: Monday, September 16, 2013 11:50:04 AM
> Subject: Re: [BioC] problem while loading affycoretools
>
> I tried all your advice: reinstall R, change mirror, still
> biocLite("affycoretools") does not install the package bit
> automatically
> and downloading the tgz from bit, the package bit does not compile
>
>
The call to chooseCRANmirror() is not persistent; you need to change mirrors every time you start R,
or do it in your ~/.Rprofile so it happens automatically every time you start R.
I don't recommend downloading files from the web and trying to install them with R CMD INSTALL. I would suggest
trying to get biocLite() working first. But for the record, a .tgz is a binary package which should already be compiled (if it contains compiled code) so I'd need to see the exact error message you are getting.
Dan
>
>
>
>
> 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 1:55 PM, Dan Tenenbaum wrote:
>
>
>
>
>
> ----- 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)'
>
>
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>
>
>
>
>
> 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
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>
> ALL OUTPUTS:
>
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>
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>
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>
>
>
>
>
> 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
>
>
>
>
>
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>
>
> 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
>
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>
>
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>
>
> 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
>
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>
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>
> 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
>
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>
>
>
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>
>
> 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
>
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>
>
>
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>
>
> 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
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>
> trying URL '
>
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> 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
>
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>
>
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>
>
> 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
>
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>
>
>
>
>
>
> 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
>
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>
>
>
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>
>
> 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
>
>
> ==================================================
>
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> downloaded 356 Kb
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> trying URL '
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> 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
>
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>
> trying URL '
>
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> 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
>
>
>
>
>
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>
>
> 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
>
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>
>
>
>
>
>
> 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
>
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>
>
>
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>
>
> 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
>
>
> ==================================================
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>
> downloaded 234 Kb
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>
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>
>
> 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
>
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>
> 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
>
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>
>
>
>
>
>
> 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
>
>
>
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> Mayte Suarez-Farinas
>
>
> Research Assistant Professor
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>
> Laboratory of Investigative Dermatology
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> Biostatistician, Center for Clinical and Translational Science
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> The Rockefeller University
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> 1230 York Ave, Box 178
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> New York, NY 10065
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> Phone: +1(212) 327-8213
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> Fax: +1(212) 327-8232
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> On Sep 16, 2013, at 1:36 PM, Dan Tenenbaum wrote:
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> ----- Original Message -----
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> From: "Mayte Suarez-Farinas" < farinam at mail.rockefeller.edu >
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> To: "James W. MacDonald" < jmacdon at uw.edu >
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> Cc: "Steve Lianoglou" < lianoglou.steve at gene.com >,
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> bioconductor at r-project.org
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> Sent: Monday, September 16, 2013 9:14:00 AM
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> Subject: Re: [BioC] problem while loading affycoretools
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> Dear James, Henrik and Steve
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> I tried biocLite("ff") and got the msg: package ‘ff’ is not available
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> (for R version 3.0.1)
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> (see below). Then I went ahead and download the tar package form
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> ( http://cran.r-project.org/web/packages/ff/index.html ) and used R
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> CMD install to install it. However,
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> while loading ff (library(ff)) it complains that the package bit was
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> missing, biocLite gave me
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> same error (package ‘bit’ is not available (for R version 3.0.1) )
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> and I could not instll via CMD install
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> gave me the following error
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> dhcp-129-85-243-253:Desktop mayte$ R CMD INSTALL bit_1.1-10.tar
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> * installing to library ‘/Users/mayte/Library/R/3.0/library’
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> * installing *source* package ‘bit’ ...
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> ** package ‘bit’ successfully unpacked and MD5 sums checked
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> ** libs
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> sh: make: command not found
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> You downloaded the source tarball for bit (.tar.gz); you wanted the
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> Mac binary (.tgz).
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> As for the problem with biocLite("bit") I'm not sure--are you behind
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> a proxy or firewall?
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> What is the output of the following:
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> library(BiocInstaller)
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> biocinstallRepos()
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> ?
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> Dan
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> ERROR: compilation failed for package ‘bit’
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> * removing ‘/Users/mayte/Library/R/3.0/library/bit’
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> dhcp-129-85-243-253:Desktop mayte$
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> Please help out, life without affycoretools is very difficult ;-)
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> From: James W. MacDonald [ jmacdon at uw.edu ]
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> Sent: Monday, September 16, 2013 11:03 AM
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> To: Mayte Suarez-Farinas
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> Cc: bioconductor at r-project.org
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> Subject: Re: [BioC] problem while loading affycoretools
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> Hi Mayte,
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> I have not seen this error in the past. Have you tried simply
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> installing
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> ff first?
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> biocLite("ff")
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> biocLite("affycoretools")
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> Best,
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> On 9/15/2013 4:57 PM, Mayte Suarez-Farinas wrote:
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> I updated to the most recent R version. After this brand new
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> installation, I get the following error while loading library
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> affycoretools:
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> library(affycoretools)
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> Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()),
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> versionCheck = vI[[j]]) :
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> there is no package called ‘ff’
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> Error: package or namespace load failed for ‘affycoretools’
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> After checking mailing list, I followed James advice
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> (
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> https://stat.ethz.ch/pipermail/bioconductor/2012-December/049895.html
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> )
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> and updated all packages
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> library(BiocInstaller)
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> biocLite(character(0))
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> Additionally, I updated all R packages as well
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> Still, the same problem arise. My R session info is bellow
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> R version 3.0.1 (2013-05-16)
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> Platform: x86_64-apple-darwin10.8.0 (64-bit)
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> locale:
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> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
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> attached base packages:
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> [1] parallel stats graphics grDevices utils datasets
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> methods base
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> other attached packages:
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> [1] KEGG.db_2.9.1 GO.db_2.9.0 RSQLite_0.11.4
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> DBI_0.2-7
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> [5] AnnotationDbi_1.22.6 affy_1.38.1 Biobase_2.20.1
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> BiocGenerics_0.6.0
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> [9] BiocInstaller_1.10.3
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> loaded via a namespace (and not attached):
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> [1] affyio_1.28.0 annaffy_1.32.0 annotate_1.38.0
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> [4] AnnotationForge_1.2.2 biomaRt_2.16.0 Biostrings_2.28.0
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> [7] Category_2.26.0 gcrma_2.32.0 gdata_2.13.2
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> [10] genefilter_1.42.0 GenomicRanges_1.12.5 GOstats_2.26.0
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> [13] gplots_2.11.3 graph_1.38.3 grid_3.0.1
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> [16] GSEABase_1.22.0 gtools_3.0.0 IRanges_1.18.3
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> [19] lattice_0.20-23 limma_3.16.7
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> preprocessCore_1.22.0
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> [22] R2HTML_2.2.1 RBGL_1.36.2 RCurl_1.95-4.1
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> [25] splines_3.0.1 stats4_3.0.1 survival_2.37-4
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> [28] tools_3.0.1 XML_3.95-0.2 xtable_1.7-1
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> [31] zlibbioc_1.6.0
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> [[alternative HTML version deleted]]
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> _______________________________________________
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> Bioconductor mailing list
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> Bioconductor at r-project.org
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> https://stat.ethz.ch/mailman/listinfo/bioconductor
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> Search the archives:
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> http://news.gmane.org/gmane.science.biology.informatics.conductor
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> --
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> James W. MacDonald, M.S.
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> Biostatistician
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> University of Washington
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> Environmental and Occupational Health Sciences
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> 4225 Roosevelt Way NE, # 100
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> Seattle WA 98105-6099
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> _______________________________________________
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> Bioconductor mailing list
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> Bioconductor at r-project.org
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> https://stat.ethz.ch/mailman/listinfo/bioconductor
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> Search the archives:
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> http://news.gmane.org/gmane.science.biology.informatics.conductor
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