Hi all,
Does anybody know what goes wrong when I receive the message
Error: evaluation is nested too deeply: infinite recursion?
during installation with getBioC() using getAllDeps=T? See the log
attached for more details.
Thanks
Claudio
Jeff Gentry wrote:
>Hello ...
>
>The latest version of getBioC() (1.2.28) involves a change to its
>parameters and not just internal improvements. This will not affect
most
>users, but for those who it will affect:
>
>- The 'isDevel' and 'version' arguments are no longer present.
>- A 'relLevel' argument has been added, which can be one of
'release',
>'devel', 'contrib', and 'release1.0'. The default is 'release',
which
>will always point ot the current release (currently 1.1). The
'contrib'
>option will install/update packages that have been contributed by the
>Bioconductor user community.
>
>-Jeff
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor@stat.math.ethz.ch
>
https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>
>
>
--
----------------------------------------------------------------------
Claudio Lottaz
Max Planck Institute for Molecular Genetics
Computational Molecular Biology Department
Ihnestrasse 73, D-14195 Berlin (Germany)
phone: +49 (0)30 8413 1177
fax: +49 (0)30 8413 1176
www:
http://www.molgen.mpg.de/~lottaz
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R : Copyright 2003, The R Development Core Team
Version 1.7.0 (2003-04-16)
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.
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Type `contributors()' for more information.
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> source('
http://www.bioconductor.org/getBioC.R')
> .libPaths('/project/gene_expression/lib/R/alpha/devel')
> getBioC(libName='all',destdir='/project/gene_expression/lib/R/alpha/
devel',relLevel='devel',getAllDeps=T)
Running getBioC version 1.2.28....
If you encounter problems, first make sure that
you are running the latest version of getBioC()
which can be found at: www.bioconductor.org/getBioC.R
Please direct any concerns or questions to
bioconductor@stat.math.ethz.ch.
[1] "Installing reposTools ..."
Creating a new generic function for "summary" in package
reposTools
Synching your local package management information ...
Packages which have been added/updated:
AnnBuilder
Biobase
DynDoc
ROC
Ruuid
SAGElyzer
affy
affycomp
annotate
dbTools
edd
genefilter
geneplotter
golubEsets
graph
hexbin
makecdfenv
marrayClasses
marrayInput
marrayNorm
marrayPlots
marrayTools
multtest
pubRepo
tkWidgets
vsn
Packages which have been removed:
KernSmooth
MASS
base
boot
class
cluster
ctest
eda
foreign
grid
lattice
lqs
methods
mgcv
modreg
mva
nlme
nls
nnet
rpart
spatial
splines
stepfun
survival
tcltk
tools
ts
Packages which have been added/updated:
KernSmooth
MASS
base
boot
class
cluster
ctest
eda
foreign
grid
lattice
lqs
methods
mgcv
modreg
mva
nlme
nls
nnet
rpart
spatial
splines
stepfun
survival
tcltk
tools
ts
Note: No specified download type, defaulting to Source
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[1] "Attempting to download reposTools from
http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing reposTools"
* Installing *source* package 'reposTools' ...
** R
** data
** inst
** help
>>> Building/Updating help pages for package 'reposTools'
Formats: text html latex example
ReposEntry-class text html latex example
ReposList-class text html latex example
VersionNumber-class text html latex example
buildPkgInfo text html latex example
buildPkgListing text html latex example
buildReposEntry text html latex example
buildVersionNumber text html latex example
buildVigDf text html latex example
checkVers text html latex example
close.locLib text html latex example
download.vignettes text html latex example
genRepos text html latex example
genReposHtml text html latex example
getLocalPkgs text html latex example
getMaxVersion text html latex example
getOptReposList text html latex example
getPkgVers text html latex example
getReplisting text html latex example
getReposEntry text html latex example
getReposList text html latex example
getRversion text html latex example
getVigDeps text html latex example
initVersionNumber text html latex
install.packages2 text html latex example
load.depends text html latex example
load.locLib text html latex example
loadRepDD text html latex example
note text html latex example
pkgInfo-class text html latex example
pkgListing-class text html latex example
pkgStatus-class text html latex example
pkgStatusList-class text html latex example
repdatadesc-class text html latex example
replisting-class text html latex example
resolve.depends text html latex example
save.locLib text html latex example
saveDfRda text html latex example
splitDFstrings text html latex example
syncLocalLibList text html latex example
unpackExtractPkgDESC text html latex example
userQuery text html latex example
winConvertSourceRepos text html latex example
* DONE (reposTools)
* DONE (INSTALL)
[1] "Installation complete"
Note: No specified download type, defaulting to Source
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[1] "Attempting to download widgetTools from
http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing widgetTools"
* Installing *source* package 'widgetTools' ...
** R
** inst
** help
>>> Building/Updating help pages for package 'widgetTools'
Formats: text html latex example
basicPW-class text html latex example
button text html latex example
makeViewer text html latex example
widget-class text html latex example
widgetView-class text html latex example
writeText text html latex example
* DONE (widgetTools)
* DONE (INSTALL)
[1] "Installation complete"
Note: No specified download type, defaulting to Source
Note: No specified download type, defaulting to Source
Note: No specified download type, defaulting to Source
Note: No specified download type, defaulting to Source
Note: No specified download type, defaulting to Source
Note: No specified download type, defaulting to Source
Note: No specified download type, defaulting to Source
Note: No specified download type, defaulting to Source
