[BioC] Error when GGtools loading

Tue Dec 14 13:11:15 CET 2010

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Some of your packages are out of date relative to this sessionInfo, so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
>
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