[BioC] trouble installing affycoretools for R 3.0

[Martin Morgan]

On 4/4/2013 2:54 PM, James W. MacDonald wrote:
> Hi Jenny,
>
> That's totally random. I wonder if there is some circular dependency that isn't
> being resolved by biocLite(). I just went through the whole rigamarole that you
> did, and in the end I get affycoretools to load, but I do get the warning about
> GenomicRanges. I don't think this should be an issue, as the package does load
> in the end, and you don't need GenomicRanges.

I think this will be fixed shortly, but a very short-term fix is 
biocLite(c("ggbio", "ggplot2")).

I think the issue is with 'ReportingTools', which uses a top-level

if(require(ggbio)){
     setMethod("objectToHTML",
         signature = signature(object = "ggbio"),
         definition = function(object, report, ...)
         {
             .doImage(object, report, ...)
         }
     )
}

'ggbio' and its dependencies (including BSgenome) are available on the build 
machine, and I think this 'require' triggers addition of objects to the 
ReportingTools name space that expect BSgenome on the user machine.

Probably ReportingTools should just Imports: ggbio, ggplot2.

Martin


>
> Best,
>
> Jim
>
>
> On 4/4/2013 4:57 PM, Zadeh, Jenny Drnevich wrote:
>>
>> 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)
>>
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>>
>> You are welcome to redistribute it under certain conditions.
>>
>> Type 'license()' or 'licence()' for distribution details.
>>
>> Natural language support but running in an English locale
>>
>> R is a collaborative project with many contributors.
>>
>> Type 'contributors()' for more information and
>>
>> 'citation()' on how to cite R or R packages in publications.
>>
>> Type 'demo()' for some demos, 'help()' for on-line help, or
>>
>> 'help.start()' for an HTML browser interface to help.
>>
>> Type 'q()' to quit R.
>>
>> > 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)
>>
>> opened URL
>>
>> downloaded 37 Kb
>>
>> 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)
>>
>> opened URL
>>
>> downloaded 2.5 Mb
>>
>> 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)
>>
>> opened URL
>>
>> downloaded 1.1 Mb
>>
>> 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)
>>
>> opened URL
>>
>> downloaded 58 Kb
>>
>> 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)
>>
>> opened URL
>>
>> downloaded 61 Kb
>>
>> 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)
>>
>> opened URL
>>
>> downloaded 92 Kb
>>
>> 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)
>>
>> opened URL
>>
>> downloaded 153 Kb
>>
>> trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/plyr_1.8.zip'
>>
>> Content type 'application/zip' length 738456 bytes (721 Kb)
>>
>> opened URL
>>
>> downloaded 721 Kb
>>
>> 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)
>>
>> opened URL
>>
>> downloaded 1.4 Mb
>>
>> 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)
>>
>> opened URL
>>
>> downloaded 2.2 Mb
>>
>> 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
>>
>> package ‘stringr’ successfully unpacked and MD5 sums checked
>>
>> package ‘munsell’ successfully unpacked and MD5 sums checked
>>
>> package ‘labeling’ successfully unpacked and MD5 sums checked
>>
>> package ‘ggplot2’ successfully unpacked and MD5 sums checked
>>
>> package ‘biovizBase’ successfully unpacked and MD5 sums checked
>>
>> package ‘reshape2’ successfully unpacked and MD5 sums checked
>>
>> package ‘gtable’ successfully unpacked and MD5 sums checked
>>
>> package ‘gridExtra’ successfully unpacked and MD5 sums checked
>>
>> package ‘scales’ successfully unpacked and MD5 sums checked
>>
>> package ‘plyr’ successfully unpacked and MD5 sums checked
>>
>> package ‘Hmisc’ successfully unpacked and MD5 sums checked
>>
>> package ‘ggbio’ successfully unpacked and MD5 sums checked
>>
>> 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 at illinois.edu
>>
>


-- 
Dr. Martin Morgan, PhD
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109