An odd issue: goseq's dependency genLenDataBase won't load in the GUI, but
loads without incident when invoked in the terminal.

GUI:

> > library(goseq)
> Loading required package: BiasedUrn
> Loading required package: geneLenDataBase
> 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 'geneLenDataBase' could not be loaded
> > sessionInfo()
> R version 2.13.0 RC (2011-04-11 r55409)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] BiasedUrn_1.03
>
> loaded via a namespace (and not attached):
>  [1] biomaRt_2.7.2        Biostrings_2.19.18   BSgenome_1.19.6
> DBI_0.2-5            GenomicRanges_1.3.38
>  [6] IRanges_1.9.31       RCurl_1.5-0          RSQLite_0.9-4
> rtracklayer_1.11.12  XML_3.2-0
>

Terminal version:

> library(goseq)
> Loading required package: BiasedUrn
> Loading required package: geneLenDataBase
> > sessionInfo()
> R version 2.13.0 RC (2011-04-11 r55409)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] goseq_1.3.3            geneLenDataBase_0.99.7 BiasedUrn_1.03
>
> loaded via a namespace (and not attached):
>  [1] AnnotationDbi_1.13.21  Biobase_2.11.10        biomaRt_2.7.2
>  [4] Biostrings_2.19.18     BSgenome_1.19.6        DBI_0.2-5
>  [7] GenomicFeatures_1.3.15 GenomicRanges_1.3.38   grid_2.13.0
> [10] IRanges_1.9.31         lattice_0.19-23        Matrix_0.999375-50
> [13] mgcv_1.7-5             nlme_3.1-100           RCurl_1.5-0
> [16] RSQLite_0.9-4          rtracklayer_1.11.12    XML_3.2-0
>

Any thoughts on this?

Eric





On Fri, Apr 8, 2011 at 1:04 PM, Berend Hasselman <bhh@xs4all.nl> wrote:

>
> On 06-04-2011, at 00:19, Simon Urbanek wrote:
>
> > It's the time of the year to test the new upcoming R release, but this
> time I'd like to ask as many users as possible to give the new R a spin,
> because there are many new features in the Mac GUI which increases the
> likelihood of bugs. It can be downloaded, as usual, from
> >
> > http://r.research.att.com/
> >
> > and for those of you that like deep links you probably want
> >
> > http://r.research.att.com/R-2.13-branch-leopard.pkg
> >
> > The new features in R itself can be found in the usual place, but this
> time the focus is also on the GUI and you can get list of new features in
> the GUI at
> > https://svn.r-project.org/R-packages/trunk/Mac-GUI/NEWS
> > Essentially the internal editor has been much re-written thanks to
> Hans-Jörg Bibiko and thus is much faster, more versatile (encoding
> selection, better auto-competion) and features shortcuts you know from Xcode
> (like <Ctrl><H> for help on the current function).
>
> I have been playing around with the editor and the Help on the current
> function.
> Ctrl+H operates reasonably well but the behaviour can be slightly strange
>
> In the examples that follow, | indicates the position of the caret.
>
> So with
>
> aggregate(d|f[.....
>
> Pressing Ctrl+H will give the help page for aggregate.
>
> However in this case
>
> aggre|gate(df[...
>
> the word aggregate is entered in the Help search field.
>
> And in this case
>
> getOption("verbose")
> suppressPackageStartupMessages(library(doBy))
> summ|aryBy(height + weight + age ~ sample, data = df, FUN = mean)
>
> with the caret within summaryBy I got help for options.
> But if the caret is in the word "library" I'll get the help page for
> message.
>
> I expected that Ctrl+H would first try to get help for the current word
> containing the caret/cursor just as it does in TextMate using the R bundle.
> And if that fails looks backwards.
>
> Berend
>
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>

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