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Question: trouble installing affycoretools for R 3.0
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gravatar for Jenny Drnevich
4.6 years ago by
Jenny Drnevich1.9k
United States
Jenny Drnevich1.9k 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/con trib/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/con trib/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/con trib/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/con trib/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/con trib/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/con trib/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/con trib/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/con trib/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/con trib/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/con trib/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/con trib/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/con trib/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/con trib/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/con trib/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/con trib/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/con trib/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/con trib/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/con trib/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/con trib/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/con trib/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/con trib/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/con trib/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/con trib/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/con trib/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/con trib/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/con trib/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/con trib/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/con trib/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/con trib/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/con trib/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/con trib/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/con trib/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/con trib/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@illinois.edu [[alternative HTML version deleted]]
ADD COMMENTlink modified 4.6 years ago by James W. MacDonald45k • written 4.6 years ago by Jenny Drnevich1.9k
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James W. MacDonald45k 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. 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/c ontrib/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/c ontrib/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/c ontrib/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/c ontrib/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 > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink written 4.6 years ago by James W. MacDonald45k
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
ADD REPLYlink written 4.6 years ago by Martin Morgan ♦♦ 20k
On Thu, Apr 4, 2013 at 3:04 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > 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")). > This is fixed now, so in a fresh R session you should be able to do: source("http://bioconductor.org/biocLite.R") biocLite("affycoretools") library(affycoretools) Without having any dependencies installed beforehand and it should work. Thanks, Dan > 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/contri b/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 > > > _______________________________________________ > 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
ADD REPLYlink written 4.6 years ago by Dan Tenenbaum ♦♦ 8.2k
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