Hello,

I installed R 3.0 today, I've been having the worst time getting all my needed packages loaded. Lots of issues, lots of problems, so I went back to the very beginning, uninstalled R 3.0 and then reinstalled it. The output below is from my first time opening R 3.0 and using biocLite() to install the base packages and then affycoretools (likely not the only problem, but one I could document well). It seems like biocLite() isn't getting all the needed packages for affycoretools - is it a problem of dependencies of dependencies? After the first sessionInfo(), I try to keep getting the packages needed to successfully load affycoretools and I have to get 4 - Bsgenome, rtracklayer, VariantAnnotation, ggbio - before library(affycoretools) don't return an Error, although I do get "No methods found in "GenomicRanges" for requests: summary". What's going on?

Thanks,
Jenny


R version 3.0.0 (2013-04-03) -- "Masked Marvel"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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  Natural language support but running in an English locale

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> source("http://bioconductor.org/biocLite.R")
trying URL 'http://www.bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/BiocInstaller_1.10.0.zip'
Content type 'application/zip' length 49954 bytes (48 Kb)
opened URL
downloaded 48 Kb

package 'BiocInstaller' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\drnevich\AppData\Local\Temp\RtmpCK5K92\downloaded_packages
Bioconductor version 2.12 (BiocInstaller 1.10.0), ?biocLite for help
> biocLite()
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.12 (BiocInstaller 1.10.0), R version 3.0.0.
Installing package(s) 'Biobase' 'IRanges' 'AnnotationDbi'
also installing the dependencies 'BiocGenerics', 'DBI', 'RSQLite'

trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/BiocGenerics_0.6.0.zip'
Content type 'application/zip' length 338146 bytes (330 Kb)
opened URL
downloaded 330 Kb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/DBI_0.2-5.zip'
Content type 'application/zip' length 394573 bytes (385 Kb)
opened URL
downloaded 385 Kb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/RSQLite_0.11.2.zip'
Content type 'application/zip' length 1115804 bytes (1.1 Mb)
opened URL
downloaded 1.1 Mb

trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/Biobase_2.20.0.zip'
Content type 'application/zip' length 2335279 bytes (2.2 Mb)
opened URL
downloaded 2.2 Mb

trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/IRanges_1.18.0.zip'
Content type 'application/zip' length 2064816 bytes (2.0 Mb)
opened URL
downloaded 2.0 Mb

trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/AnnotationDbi_1.22.0.zip'
Content type 'application/zip' length 4148969 bytes (4.0 Mb)
opened URL
downloaded 4.0 Mb

package 'BiocGenerics' successfully unpacked and MD5 sums checked
package 'DBI' successfully unpacked and MD5 sums checked
package 'RSQLite' successfully unpacked and MD5 sums checked
package 'Biobase' successfully unpacked and MD5 sums checked
package 'IRanges' successfully unpacked and MD5 sums checked
package 'AnnotationDbi' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\drnevich\AppData\Local\Temp\RtmpCK5K92\downloaded_packages
> biocLite("affycoretools")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.12 (BiocInstaller 1.10.0), R version 3.0.0.
Installing package(s) 'affycoretools'
also installing the dependencies 'bitops', 'org.Hs.eg.db', 'bit', 'iterators', 'R.oo', 'R.methodsS3', 'affyio', 'preprocessCore', 'zlibbioc', 'XML', 'RCurl', 'Category', 'graph', 'RBGL', 'AnnotationForge', 'Biostrings', 'gtools', 'gdata', 'caTools', 'GenomicRanges', 'ff', 'foreach', 'edgeR', 'PFAM.db', 'GSEABase', 'R.utils', 'affy', 'GO.db', 'KEGG.db', 'biomaRt', 'limma', 'GOstats', 'annotate', 'annaffy', 'genefilter', 'gcrma', 'xtable', 'gplots', 'R2HTML', 'oligoClasses', 'ReportingTools', 'hwriter'

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/bitops_1.0-5.zip'
Content type 'application/zip' length 35558 bytes (34 Kb)
opened URL
downloaded 34 Kb

trying URL 'http://bioconductor.org/packages/2.12/data/annotation/bin/windows/contrib/3.0/org.Hs.eg.db_2.9.0.zip'
Content type 'application/zip' length 53311411 bytes (50.8 Mb)
opened URL
downloaded 50.8 Mb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/bit_1.1-10.zip'
Content type 'application/zip' length 209778 bytes (204 Kb)
opened URL
downloaded 204 Kb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/iterators_1.0.6.zip'
Content type 'application/zip' length 317664 bytes (310 Kb)
opened URL
downloaded 310 Kb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/R.oo_1.13.0.zip'
Content type 'application/zip' length 761201 bytes (743 Kb)
opened URL
downloaded 743 Kb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/R.methodsS3_1.4.2.zip'
Content type 'application/zip' length 51675 bytes (50 Kb)
opened URL
downloaded 50 Kb

trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/affyio_1.28.0.zip'
Content type 'application/zip' length 161896 bytes (158 Kb)
opened URL
downloaded 158 Kb

trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/preprocessCore_1.22.0.zip'
Content type 'application/zip' length 204423 bytes (199 Kb)
opened URL
downloaded 199 Kb

trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/zlibbioc_1.6.0.zip'
Content type 'application/zip' length 246818 bytes (241 Kb)
opened URL
downloaded 241 Kb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/XML_3.96-1.1.zip'
Content type 'application/zip' length 4253990 bytes (4.1 Mb)
opened URL
downloaded 4.1 Mb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/RCurl_1.95-4.1.zip'
Content type 'application/zip' length 2834597 bytes (2.7 Mb)
opened URL
downloaded 2.7 Mb

trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/Category_2.26.0.zip'
Content type 'application/zip' length 906831 bytes (885 Kb)
opened URL
downloaded 885 Kb

trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/graph_1.38.0.zip'
Content type 'application/zip' length 1364168 bytes (1.3 Mb)
opened URL
downloaded 1.3 Mb

trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/RBGL_1.36.0.zip'
Content type 'application/zip' length 1565728 bytes (1.5 Mb)
opened URL
downloaded 1.5 Mb

trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/AnnotationForge_1.2.0.zip'
Content type 'application/zip' length 4345633 bytes (4.1 Mb)
opened URL
downloaded 4.1 Mb

trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/Biostrings_2.28.0.zip'
Content type 'application/zip' length 2297147 bytes (2.2 Mb)
opened URL
downloaded 2.2 Mb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/gtools_2.7.1.zip'
Content type 'application/zip' length 106961 bytes (104 Kb)
opened URL
downloaded 104 Kb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/gdata_2.12.0.1.zip'
Content type 'application/zip' length 844869 bytes (825 Kb)
opened URL
downloaded 825 Kb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/caTools_1.14.zip'
Content type 'application/zip' length 227479 bytes (222 Kb)
opened URL
downloaded 222 Kb

trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/GenomicRanges_1.12.0.zip'
Content type 'application/zip' length 3302501 bytes (3.1 Mb)
opened URL
downloaded 3.1 Mb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/ff_2.2-11.zip'
Content type 'application/zip' length 1457738 bytes (1.4 Mb)
opened URL
downloaded 1.4 Mb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/foreach_1.4.0.zip'
Content type 'application/zip' length 390455 bytes (381 Kb)
opened URL
downloaded 381 Kb

trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/edgeR_3.2.0.zip'
Content type 'application/zip' length 1893338 bytes (1.8 Mb)
opened URL
downloaded 1.8 Mb

trying URL 'http://bioconductor.org/packages/2.12/data/annotation/bin/windows/contrib/3.0/PFAM.db_2.9.0.zip'
Content type 'application/zip' length 2353344 bytes (2.2 Mb)
opened URL
downloaded 2.2 Mb

trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/GSEABase_1.22.0.zip'
Content type 'application/zip' length 599017 bytes (584 Kb)
opened URL
downloaded 584 Kb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/R.utils_1.23.2.zip'
Content type 'application/zip' length 871369 bytes (850 Kb)
opened URL
downloaded 850 Kb

trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/affy_1.38.0.zip'
Content type 'application/zip' length 1467209 bytes (1.4 Mb)
opened URL
downloaded 1.4 Mb

trying URL 'http://bioconductor.org/packages/2.12/data/annotation/bin/windows/contrib/3.0/GO.db_2.9.0.zip'
Content type 'application/zip' length 25091062 bytes (23.9 Mb)
opened URL
downloaded 23.9 Mb

trying URL 'http://bioconductor.org/packages/2.12/data/annotation/bin/windows/contrib/3.0/KEGG.db_2.9.0.zip'
Content type 'application/zip' length 2097901 bytes (2.0 Mb)
opened URL
downloaded 2.0 Mb

trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/biomaRt_2.16.0.zip'
Content type 'application/zip' length 346992 bytes (338 Kb)
opened URL
downloaded 338 Kb

trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/limma_3.16.0.zip'
Content type 'application/zip' length 1579932 bytes (1.5 Mb)
opened URL
downloaded 1.5 Mb

trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/GOstats_2.26.0.zip'
Content type 'application/zip' length 1713103 bytes (1.6 Mb)
opened URL
downloaded 1.6 Mb

trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/annotate_1.38.0.zip'
Content type 'application/zip' length 1939134 bytes (1.8 Mb)
opened URL
downloaded 1.8 Mb

trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/annaffy_1.32.0.zip'
Content type 'application/zip' length 386071 bytes (377 Kb)
opened URL
downloaded 377 Kb

trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/genefilter_1.42.0.zip'
Content type 'application/zip' length 1160782 bytes (1.1 Mb)
opened URL
downloaded 1.1 Mb

trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/gcrma_2.32.0.zip'
Content type 'application/zip' length 244429 bytes (238 Kb)
opened URL
downloaded 238 Kb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/xtable_1.7-1.zip'
Content type 'application/zip' length 378269 bytes (369 Kb)
opened URL
downloaded 369 Kb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/gplots_2.11.0.1.zip'
Content type 'application/zip' length 334998 bytes (327 Kb)
opened URL
downloaded 327 Kb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/R2HTML_2.2.zip'
Content type 'application/zip' length 448252 bytes (437 Kb)
opened URL
downloaded 437 Kb

trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/oligoClasses_1.22.0.zip'
Content type 'application/zip' length 883030 bytes (862 Kb)
opened URL
downloaded 862 Kb

trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/ReportingTools_2.0.0.zip'
Content type 'application/zip' length 2176145 bytes (2.1 Mb)
opened URL
downloaded 2.1 Mb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/hwriter_1.3.zip'
Content type 'application/zip' length 138415 bytes (135 Kb)
opened URL
downloaded 135 Kb

trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/affycoretools_1.32.0.zip'
Content type 'application/zip' length 7054128 bytes (6.7 Mb)
opened URL
downloaded 6.7 Mb

package 'bitops' successfully unpacked and MD5 sums checked
package 'bit' successfully unpacked and MD5 sums checked
package 'iterators' successfully unpacked and MD5 sums checked
package 'R.oo' successfully unpacked and MD5 sums checked
package 'R.methodsS3' successfully unpacked and MD5 sums checked
package 'affyio' successfully unpacked and MD5 sums checked
package 'preprocessCore' successfully unpacked and MD5 sums checked
package 'zlibbioc' successfully unpacked and MD5 sums checked
package 'XML' successfully unpacked and MD5 sums checked
package 'RCurl' successfully unpacked and MD5 sums checked
package 'Category' successfully unpacked and MD5 sums checked
package 'graph' successfully unpacked and MD5 sums checked
package 'RBGL' successfully unpacked and MD5 sums checked
package 'AnnotationForge' successfully unpacked and MD5 sums checked
package 'Biostrings' successfully unpacked and MD5 sums checked
package 'gtools' successfully unpacked and MD5 sums checked
package 'gdata' successfully unpacked and MD5 sums checked
package 'caTools' successfully unpacked and MD5 sums checked
package 'GenomicRanges' successfully unpacked and MD5 sums checked
package 'ff' successfully unpacked and MD5 sums checked
package 'foreach' successfully unpacked and MD5 sums checked
package 'edgeR' successfully unpacked and MD5 sums checked
package 'GSEABase' successfully unpacked and MD5 sums checked
package 'R.utils' successfully unpacked and MD5 sums checked
package 'affy' successfully unpacked and MD5 sums checked
package 'biomaRt' successfully unpacked and MD5 sums checked
package 'limma' successfully unpacked and MD5 sums checked
package 'GOstats' successfully unpacked and MD5 sums checked
package 'annotate' successfully unpacked and MD5 sums checked
package 'annaffy' successfully unpacked and MD5 sums checked
package 'genefilter' successfully unpacked and MD5 sums checked
package 'gcrma' successfully unpacked and MD5 sums checked
package 'xtable' successfully unpacked and MD5 sums checked
package 'gplots' successfully unpacked and MD5 sums checked
package 'R2HTML' successfully unpacked and MD5 sums checked
package 'oligoClasses' successfully unpacked and MD5 sums checked
package 'ReportingTools' successfully unpacked and MD5 sums checked
package 'hwriter' successfully unpacked and MD5 sums checked
package 'affycoretools' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\drnevich\AppData\Local\Temp\RtmpCK5K92\downloaded_packages
> library(affycoretools)
Loading required package: affy
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:stats':

    xtabs

The following objects are masked from 'package:base':

    anyDuplicated, as.data.frame, cbind, colnames, duplicated, eval,
    Filter, Find, get, intersect, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unlist

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: DBI

Loading required package: KEGG.db

KEGG.db contains mappings based on older data because the original
  resource was removed from the the public domain before the most
  recent update was produced. This package should now be considered
  deprecated and future versions of Bioconductor may not have it
  available.  One possible alternative to consider is to look at the
  reactome.db package


Error in loadNamespace(name) : there is no package called 'BSgenome'
Error: package or namespace load failed for 'affycoretools'
> sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages:
[1] KEGG.db_2.9.0        GO.db_2.9.0          RSQLite_0.11.2
[4] DBI_0.2-5            AnnotationDbi_1.22.0 affy_1.38.0
[7] Biobase_2.20.0       BiocGenerics_0.6.0   BiocInstaller_1.10.0

loaded via a namespace (and not attached):
[1] affyio_1.28.0         annaffy_1.32.0        annotate_1.38.0
 [4] AnnotationForge_1.2.0 biomaRt_2.16.0        Biostrings_2.28.0
 [7] bit_1.1-10            Category_2.26.0       codetools_0.2-8
[10] edgeR_3.2.0           ff_2.2-11             foreach_1.4.0
[13] gcrma_2.32.0          gdata_2.12.0.1        genefilter_1.42.0
[16] GenomicRanges_1.12.0  GOstats_2.26.0        gplots_2.11.0.1
[19] graph_1.38.0          grid_3.0.0            GSEABase_1.22.0
[22] gtools_2.7.1          hwriter_1.3           IRanges_1.18.0
[25] iterators_1.0.6       lattice_0.20-15       limma_3.16.0
[28] oligoClasses_1.22.0   PFAM.db_2.9.0         preprocessCore_1.22.0
[31] R.methodsS3_1.4.2     R.oo_1.13.0           R.utils_1.23.2
[34] R2HTML_2.2            RBGL_1.36.0           RCurl_1.95-4.1
[37] splines_3.0.0         stats4_3.0.0          survival_2.37-4
[40] tools_3.0.0           XML_3.96-1.1          xtable_1.7-1
[43] zlibbioc_1.6.0
> biocLite("BSgenome")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.12 (BiocInstaller 1.10.0), R version 3.0.0.
Installing package(s) 'BSgenome'
trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/BSgenome_1.28.0.zip'
Content type 'application/zip' length 775534 bytes (757 Kb)
opened URL
downloaded 757 Kb

package 'BSgenome' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\drnevich\AppData\Local\Temp\RtmpCK5K92\downloaded_packages
> library(affycoretools)
Error in loadNamespace(name) : there is no package called 'rtracklayer'
Error: package or namespace load failed for 'affycoretools'
> biocLite("rtracklayer")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.12 (BiocInstaller 1.10.0), R version 3.0.0.
Installing package(s) 'rtracklayer'
also installing the dependency 'Rsamtools'

trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/Rsamtools_1.12.0.zip'
Content type 'application/zip' length 3906419 bytes (3.7 Mb)
opened URL
downloaded 3.7 Mb

trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/rtracklayer_1.20.0.zip'
Content type 'application/zip' length 1789773 bytes (1.7 Mb)
opened URL
downloaded 1.7 Mb

package 'Rsamtools' successfully unpacked and MD5 sums checked
package 'rtracklayer' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\drnevich\AppData\Local\Temp\RtmpCK5K92\downloaded_packages
> library(affycoretools)
Error in loadNamespace(name) :
  there is no package called 'VariantAnnotation'
Error: package or namespace load failed for 'affycoretools'
> biocLite("VariantAnnotation")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.12 (BiocInstaller 1.10.0), R version 3.0.0.
Installing package(s) 'VariantAnnotation'
also installing the dependency 'GenomicFeatures'

trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/GenomicFeatures_1.12.0.zip'
Content type 'application/zip' length 971493 bytes (948 Kb)
opened URL
downloaded 948 Kb

trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/VariantAnnotation_1.6.0.zip'
Content type 'application/zip' length 1762582 bytes (1.7 Mb)
opened URL
downloaded 1.7 Mb

package 'GenomicFeatures' successfully unpacked and MD5 sums checked
package 'VariantAnnotation' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\drnevich\AppData\Local\Temp\RtmpCK5K92\downloaded_packages
> library(affycoretools)
Error in loadNamespace(name) : there is no package called 'ggbio'
Error: package or namespace load failed for 'affycoretools'
> biocLite("ggbio")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.12 (BiocInstaller 1.10.0), R version 3.0.0.
Installing package(s) 'ggbio'
also installing the dependencies 'colorspace', 'digest', 'proto', 'RColorBrewer', 'dichromat', 'stringr', 'munsell', 'labeling', 'ggplot2', 'biovizBase', 'reshape2', 'gtable', 'gridExtra', 'scales', 'plyr', 'Hmisc'

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/colorspace_1.2-1.zip'
Content type 'application/zip' length 382086 bytes (373 Kb)
opened URL
downloaded 373 Kb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/digest_0.6.3.zip'
Content type 'application/zip' length 136316 bytes (133 Kb)
opened URL
downloaded 133 Kb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/proto_0.3-10.zip'
Content type 'application/zip' length 458271 bytes (447 Kb)
opened URL
downloaded 447 Kb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/RColorBrewer_1.0-5.zip'
Content type 'application/zip' length 25286 bytes (24 Kb)
opened URL
downloaded 24 Kb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/dichromat_2.0-0.zip'
Content type 'application/zip' length 147536 bytes (144 Kb)
opened URL
downloaded 144 Kb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/stringr_0.6.2.zip'
Content type 'application/zip' length 74542 bytes (72 Kb)
opened URL
downloaded 72 Kb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/munsell_0.4.zip'
Content type 'application/zip' length 125748 bytes (122 Kb)
opened URL
downloaded 122 Kb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/labeling_0.1.zip'
Content type 'application/zip' length 38052 bytes (37 Kb)
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trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/ggplot2_0.9.3.1.zip'
Content type 'application/zip' length 2652129 bytes (2.5 Mb)
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trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/biovizBase_1.8.0.zip'
Content type 'application/zip' length 1155844 bytes (1.1 Mb)
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trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/reshape2_1.2.2.zip'
Content type 'application/zip' length 59866 bytes (58 Kb)
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trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/gtable_0.1.2.zip'
Content type 'application/zip' length 62953 bytes (61 Kb)
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trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/gridExtra_0.9.1.zip'
Content type 'application/zip' length 94629 bytes (92 Kb)
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trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/scales_0.2.3.zip'
Content type 'application/zip' length 157415 bytes (153 Kb)
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trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/plyr_1.8.zip'
Content type 'application/zip' length 738456 bytes (721 Kb)
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trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/Hmisc_3.10-1.zip'
Content type 'application/zip' length 1457136 bytes (1.4 Mb)
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trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/ggbio_1.8.0.zip'
Content type 'application/zip' length 2270016 bytes (2.2 Mb)
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package 'colorspace' successfully unpacked and MD5 sums checked
package 'digest' successfully unpacked and MD5 sums checked
package 'proto' successfully unpacked and MD5 sums checked
package 'RColorBrewer' successfully unpacked and MD5 sums checked
package 'dichromat' successfully unpacked and MD5 sums checked
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The downloaded binary packages are in
        C:\Users\drnevich\AppData\Local\Temp\RtmpCK5K92\downloaded_packages
> library(affycoretools)
No methods found in "GenomicRanges" for requests: summary
> sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages:
[1] affycoretools_1.32.0 KEGG.db_2.9.0        GO.db_2.9.0          RSQLite_0.11.2
 [5] DBI_0.2-5            AnnotationDbi_1.22.0 affy_1.38.0          Biobase_2.20.0
 [9] BiocGenerics_0.6.0   BiocInstaller_1.10.0

loaded via a namespace (and not attached):
[1] affyio_1.28.0           annaffy_1.32.0          annotate_1.38.0
 [4] AnnotationForge_1.2.0   biomaRt_2.16.0          Biostrings_2.28.0
 [7] biovizBase_1.8.0        bit_1.1-10              bitops_1.0-5
[10] BSgenome_1.28.0         Category_2.26.0         cluster_1.14.4
[13] codetools_0.2-8         colorspace_1.2-1        dichromat_2.0-0
[16] digest_0.6.3            edgeR_3.2.0             ff_2.2-11
[19] foreach_1.4.0           gcrma_2.32.0            gdata_2.12.0.1
[22] genefilter_1.42.0       GenomicFeatures_1.12.0  GenomicRanges_1.12.0
[25] ggbio_1.8.0             ggplot2_0.9.3.1         GOstats_2.26.0
[28] gplots_2.11.0.1         graph_1.38.0            grid_3.0.0
[31] gridExtra_0.9.1         GSEABase_1.22.0         gtable_0.1.2
[34] gtools_2.7.1            Hmisc_3.10-1            hwriter_1.3
[37] IRanges_1.18.0          iterators_1.0.6         labeling_0.1
[40] lattice_0.20-15         limma_3.16.0            MASS_7.3-26
[43] munsell_0.4             oligoClasses_1.22.0     PFAM.db_2.9.0
[46] plyr_1.8                preprocessCore_1.22.0   proto_0.3-10
[49] R.methodsS3_1.4.2       R.oo_1.13.0             R.utils_1.23.2
[52] R2HTML_2.2              RBGL_1.36.0             RColorBrewer_1.0-5
[55] RCurl_1.95-4.1          ReportingTools_2.0.0    reshape2_1.2.2
[58] Rsamtools_1.12.0        rtracklayer_1.20.0      scales_0.2.3
[61] splines_3.0.0           stats4_3.0.0            stringr_0.6.2
[64] survival_2.37-4         tools_3.0.0             VariantAnnotation_1.6.0
[67] XML_3.96-1.1            xtable_1.7-1            zlibbioc_1.6.0
>


Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
High Performance Biological Computing Program
and The Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

NOTE NEW OFFICE LOCATION
2112 IGB
1206 W. Gregory Dr.
Urbana, IL 61801
USA
ph: 217-300-6543
fax: 217-265-5066
e-mail: drnevich@illinois.edu


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