Dear bioconductors, I got error when I intent to load GGtools. It has been installed. I need your helps on fix this problem. Thanks in advance. > library(GGtools) Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: GGBase Loading required package: snpMatrix Loading required package: survival Loading required package: splines Loading required package: RSQLite Loading required package: DBI Loading required package: annotate Loading required package: AnnotationDbi Loading required package: IRanges Attaching package: 'IRanges' The following object(s) are masked from 'package:Biobase': updateObject The following object(s) are masked from 'package:base': Map, cbind, eval, mapply, order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int, table Loading required package: rtracklayer Loading required package: RCurl Loading required package: bitops Loading required package: org.Hs.eg.db Loading required package: GenomicRanges Loading required package: ff Loading required package: tools Loading required package: bit Loading package bit1.1-6 package:bit (c) 2008/2009 Jens Oehlschlaegel (GPL-2) creators: bit bitwhich coercion: as.logical as.integer as.bit as.bitwhich which operator: ! & | xor != == querying: print length any all min max range sum summary bit access: length<- [ [<- [[ [[<- for more help type ?bit Attaching package: 'bit' The following object(s) are masked from 'package:base': xor Loading package ff2.2-1 - getOption("fftempdir")=="/var/folders/Ic/IcbLL0ELH9uqwZPaFP9Nz++++TQ /-Tmp-//RtmpXEoKMB" - getOption("ffextension")=="ff" - getOption("ffdrop")==TRUE - getOption("fffinonexit")==TRUE - getOption("ffpagesize")==65536 - getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes - getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system - getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system Attaching package ff Attaching package: 'ff' The following object(s) are masked from 'package:utils': write.csv, write.csv2 The following object(s) are masked from 'package:base': is.factor, is.ordered Error in as.environment(pos) : no item called "newtable" on the search list In addition: Warning message: In objects(newtable, all.names = TRUE) : ?newtable? converted to character string Error: package/namespace load failed for 'GGtools' > search() [1] ".GlobalEnv" "package:ff" "package:bit" [4] "package:tools" "package:GenomicRanges" "package:org.Hs.eg.db" [7] "package:rtracklayer" "package:RCurl" "package:bitops" [10] "package:IRanges" "package:annotate" "package:AnnotationDbi" [13] "package:GGBase" "package:RSQLite" "package:DBI" [16] "package:snpMatrix" "package:survival" "package:splines" [19] "package:Biobase" "package:stats" "package:graphics" [22] "package:grDevices" "package:utils" "package:datasets" [25] "package:methods" "Autoloads" "package:base" > version _ platform x86_64-apple-darwin9.8.0 arch x86_64 os darwin9.8.0 system x86_64, darwin9.8.0 status major 2 minor 12.0 year 2010 month 10 day 15 svn rev 53317 language R version.string R version 2.12.0 (2010-10-15) > package.skeleton("GGtools") Creating directories ... Creating DESCRIPTION ... Creating Read-and-delete-me ... Saving functions and data ... Making help files ... Done. Further steps are described in './GGtools/Read-and-delete-me'. > sessionInfo() R version 2.12.0 (2010-10-15) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C/UTF-8/C/C/C/C attached base packages: [1] tools splines stats graphics grDevices utils datasets [8] methods base other attached packages: [1] ff_2.2-1 bit_1.1-6 GenomicRanges_1.2.1 [4] org.Hs.eg.db_2.4.6 rtracklayer_1.10.6 RCurl_1.4-3 [7] bitops_1.0-4.1 IRanges_1.8.7 annotate_1.28.0 [10] AnnotationDbi_1.12.0 GGBase_3.10.0 RSQLite_0.9-4 [13] DBI_0.2-5 snpMatrix_1.14.0 survival_2.36-2 [16] Biobase_2.10.0 loaded via a namespace (and not attached): [1] BSgenome_1.18.2 Biostrings_2.18.0 GSEABase_1.12.1 XML_3.2-0 [5] annaffy_1.22.0 graph_1.28.0 xtable_1.5-6 Jian-Feng

I have seen this error before and it has been somewhat challenging to get around. Here is my sessionInfo, for a mac running OSX 10.6.4 -- yours seems to be a bit older R version 2.12.0 Patched (2010-11-28 r53696) Platform: x86_64-apple-darwin10.4.0/x86_64 (64-bit) locale: [1] C attached base packages: [1] splines stats graphics grDevices datasets tools utils [8] methods base other attached packages: [1] GGtools_3.8.4 ff_2.2-1 bit_1.1-6 [4] GenomicRanges_1.2.2 org.Hs.eg.db_2.4.6 rtracklayer_1.10.6 [7] RCurl_1.5-0 bitops_1.0-4.1 IRanges_1.8.7 [10] annotate_1.28.0 AnnotationDbi_1.12.0 GGBase_3.10.0 [13] RSQLite_0.9-4 DBI_0.2-5 snpMatrix_1.14.0 [16] survival_2.36-2 Biobase_2.10.0 weaver_1.16.0 [19] codetools_0.2-6 digest_0.4.2 loaded via a namespace (and not attached): [1] BSgenome_1.18.2 Biostrings_2.18.2 GSEABase_1.12.1 XML_3.2-0 [5] annaffy_1.22.0 graph_1.28.0 xtable_1.5-6 Some of your packages are out of date relative to this sessionInfo, so update.packages(repos=biocinstallRepos()) may help. You might consider updating your MacOSX version and the associated Xcode tools (in the past this problem seemed related to uuid infrastructure). Also tell me whether you are building from source or using the R GUI for MacOSX. I will try to reproduce it but it will be hard without a darwin9.8 machine which I don't think I can get my hands on. On Tue, Dec 14, 2010 at 6:15 AM, Mao Jianfeng <jianfeng.mao at="" gmail.com=""> wrote: > Dear bioconductors, > > I got error when I intent to load GGtools. It has been installed. I > need your ?helps on fix this problem. Thanks in advance. > >> library(GGtools) > Loading required package: Biobase > > Welcome to Bioconductor > > ?Vignettes contain introductory material. To view, type > ?'openVignette()'. To cite Bioconductor, see > ?'citation("Biobase")' and for packages 'citation(pkgname)'. > > Loading required package: GGBase > Loading required package: snpMatrix > Loading required package: survival > Loading required package: splines > Loading required package: RSQLite > Loading required package: DBI > Loading required package: annotate > Loading required package: AnnotationDbi > Loading required package: IRanges > > Attaching package: 'IRanges' > > The following object(s) are masked from 'package:Biobase': > > ? ?updateObject > > The following object(s) are masked from 'package:base': > > ? ?Map, cbind, eval, mapply, order, paste, pmax, pmax.int, pmin, > ? ?pmin.int, rbind, rep.int, table > > Loading required package: rtracklayer > Loading required package: RCurl > Loading required package: bitops > Loading required package: org.Hs.eg.db > Loading required package: GenomicRanges > Loading required package: ff > Loading required package: tools > Loading required package: bit > Loading package bit1.1-6 > > package:bit (c) 2008/2009 Jens Oehlschlaegel (GPL-2) > > creators: bit bitwhich > > coercion: as.logical as.integer as.bit as.bitwhich which > > operator: ! & | xor != == > > querying: print length any all min max range sum summary > > bit access: length<- [ [<- [[ [[<- > > for more help type ?bit > > > Attaching package: 'bit' > > The following object(s) are masked from 'package:base': > > ? ?xor > > Loading package ff2.2-1 > > - getOption("fftempdir")=="/var/folders/Ic/IcbLL0ELH9uqwZPaFP9Nz++++ TQ/-Tmp-//RtmpXEoKMB" > > - getOption("ffextension")=="ff" > > - getOption("ffdrop")==TRUE > > - getOption("fffinonexit")==TRUE > > - getOption("ffpagesize")==65536 > > - getOption("ffcaching")=="mmnoflush" ?-- consider "ffeachflush" if > your system stalls on large writes > > - getOption("ffbatchbytes")==16777216 -- consider a different value > for tuning your system > > - getOption("ffmaxbytes")==536870912 -- consider a different value for > tuning your system > > Attaching package ff > > > Attaching package: 'ff' > > The following object(s) are masked from 'package:utils': > > ? ?write.csv, write.csv2 > > The following object(s) are masked from 'package:base': > > ? ?is.factor, is.ordered > > Error in as.environment(pos) : > ?no item called "newtable" on the search list > In addition: Warning message: > In objects(newtable, all.names = TRUE) : > ??newtable? converted to character string > Error: package/namespace load failed for 'GGtools' > >> search() > ?[1] ".GlobalEnv" ? ? ? ? ? ?"package:ff" ? ? ? ? ? ?"package:bit" > ?[4] "package:tools" ? ? ? ? "package:GenomicRanges" "package:org.Hs.eg.db" > ?[7] "package:rtracklayer" ? "package:RCurl" ? ? ? ? "package:bitops" > [10] "package:IRanges" ? ? ? "package:annotate" ? ? ?"package:AnnotationDbi" > [13] "package:GGBase" ? ? ? ?"package:RSQLite" ? ? ? "package:DBI" > [16] "package:snpMatrix" ? ? "package:survival" ? ? ?"package:splines" > [19] "package:Biobase" ? ? ? "package:stats" ? ? ? ? "package:graphics" > [22] "package:grDevices" ? ? "package:utils" ? ? ? ? "package:datasets" > [25] "package:methods" ? ? ? "Autoloads" ? ? ? ? ? ? "package:base" > >> version > ? ? ? ? ? ? ? _ > platform ? ? ? x86_64-apple-darwin9.8.0 > arch ? ? ? ? ? x86_64 > os ? ? ? ? ? ? darwin9.8.0 > system ? ? ? ? x86_64, darwin9.8.0 > status > major ? ? ? ? ?2 > minor ? ? ? ? ?12.0 > year ? ? ? ? ? 2010 > month ? ? ? ? ?10 > day ? ? ? ? ? ?15 > svn rev ? ? ? ?53317 > language ? ? ? R > version.string R version 2.12.0 (2010-10-15) > >> package.skeleton("GGtools") > Creating directories ... > Creating DESCRIPTION ... > Creating Read-and-delete-me ... > Saving functions and data ... > Making help files ... > Done. > Further steps are described in './GGtools/Read-and-delete-me'. >> sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] C/UTF-8/C/C/C/C > > attached base packages: > [1] tools ? ? splines ? stats ? ? graphics ?grDevices utils ? ? datasets > [8] methods ? base > > other attached packages: > ?[1] ff_2.2-1 ? ? ? ? ? ? bit_1.1-6 ? ? ? ? ? ?GenomicRanges_1.2.1 > ?[4] org.Hs.eg.db_2.4.6 ? rtracklayer_1.10.6 ? RCurl_1.4-3 > ?[7] bitops_1.0-4.1 ? ? ? IRanges_1.8.7 ? ? ? ?annotate_1.28.0 > [10] AnnotationDbi_1.12.0 GGBase_3.10.0 ? ? ? ?RSQLite_0.9-4 > [13] DBI_0.2-5 ? ? ? ? ? ?snpMatrix_1.14.0 ? ? survival_2.36-2 > [16] Biobase_2.10.0 > > loaded via a namespace (and not attached): > [1] BSgenome_1.18.2 ? Biostrings_2.18.0 GSEABase_1.12.1 ? XML_3.2-0 > [5] annaffy_1.22.0 ? ?graph_1.28.0 ? ? ?xtable_1.5-6 > > Jian-Feng > > _______________________________________________ > 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 >