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