[BioC] Error when GGtools loading

Mao Jianfeng jianfeng.mao at gmail.com
Tue Dec 14 12:15:08 CET 2010

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':


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':


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
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 ...
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)

[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


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