[Bioc-devel] Problem with getBioC(develOK=TRUE)
Goeman, J.J. (MSTAT)
J.J.Goeman at lumc.nl
Wed Oct 13 11:52:21 CEST 2004
Hi Robert,
My reposTools version is the same as yours. I went trough getBioC to track
down the problem. It is somewhere here:
## FIXME:
## Despite using themes, still need to go through
## this headache right now because we're doing an
## update and then an install to pick up any new
## values. Need to have functionality like the old
## install.packages2() which only updates old
## packages and installs new packages built into
## reposTools. So we're only pseudo-using themes
## right now.
repThemes <- reposThemes(bioCEntries)
themeNames <- unlist(lapply(repThemes, repThemeName))
print("Test:")
print(themeNames)
whichTheme <- match(libName, themeNames)
if (is.na(whichTheme))
stop(packNameOutput())
packs <-
unlist(lapply(repThemePkgs(repThemes[[whichTheme]]),
pkgName))
When I get to this part, I get these values, which do not seem right to me.
> repThemes
list()
> themeNames
NULL
> whichTheme
[1] NA
The functon prints "Test:", then all possible options for libName, then
quits.
Best wishes,
Jelle
http://www.math.leidenuniv.nl/~jgoeman
> -----Original Message-----
> From: Robert Gentleman [mailto:rgentlem at jimmy.harvard.edu]
> Sent: Wednesday, 13 October, 2004 11:22 AM
> To: Goeman, J.J. (MSTAT)
> Subject: Re: [BioC] problems with getBioC() and
> getBioC(develOK=TRUE) on
> R 2.0.0
>
>
>
> On Wed, Oct 13, 2004 at 10:46:15AM +0200, Goeman, J.J. (MSTAT) wrote:
> > Hi Robert,
> >
> > I also get errors (different ones) if I try installing the
> develOK branch;
> > see the second part of the email.
>
> Yes, and I suspect that you have installed the wrong version of
> reposTools - so perhaps if you try first doing a remove.packages
> (you might find this out by starting R, and going
> library(reposTools)
> and see if that works - it looks like somehow your version is
> interacting badly with getBioC.
>
> I get:
> packageDescription("reposTools")$Version
>
> [1] "1.4.11"
>
> Otherwise, you can take the getBioC script and go through it one
> line at a time, and figure out where it fails, we can fix it given a
> report.
>
>
> Robert
> >
> > Jelle
> >
> > http://www.math.leidenuniv.nl/~jgoeman
> >
> > > -----Original Message-----
> > > From: Robert Gentleman [mailto:rgentlem at jimmy.harvard.edu]
> > > Sent: Wednesday, 13 October, 2004 10:33 AM
> > > To: Goeman, J.J. (MSTAT)
> > > Cc: 'bioconductor at stat.math.ethz.ch'
> > > Subject: Re: [BioC] problems with getBioC() and
> > > getBioC(develOK=TRUE) on
> > > R 2.0.0
> > >
> > >
> > > Yes, and it is rather unfortunate, but actually well
> > > documented. Please, if you want to use Bioconductor with
> R 2.0.0 you
> > > *must* use the devel branch, or you can use R 1.9.1 with
> the release
> > > branch. The next release is a few weeks away, but there
> is a necessary
> > > lag between R releases and BioC releases.
> > >
> > > Robert
> > >
> > > On Wed, Oct 13, 2004 at 10:28:50AM +0200, Goeman, J.J.
> (MSTAT) wrote:
> > > > Hi,
> > > >
> > > > I'm trying to install Bioconductor on R 2.0.0 (windows
> > > version). I get some
> > > > strange errors
> > > >
> > > > I first try the release version:
> > > >
> > > > > source("http://www.bioconductor.org/getBioC.R")
> > > > > getBioC()
> > > > Running getBioC version 1.2.65....
> > > > 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 at stat.math.ethz.ch.
> > > >
> > > > [1] "Installing reposTools ..."
> > > > Loading required package: reposTools
> > > > Error in library(package, character.only = TRUE, logical = TRUE,
> > > > warn.conflicts = warn.conflicts, :
> > > > 'reposTools' is not a valid package --
> installed < 2.0.0?
> > > >
> > > > Maybe I shouldn't use the release version on 2.0.0?
> Then I try the
> > > > developmental version:
> > > >
> > > > > getBioC(develOK=TRUE)
> > > > Running getBioC version 1.2.65....
> > > > 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 at stat.math.ethz.ch.
> > > >
> > > > [1] "Installing reposTools ..."
> > > > Loading required package: reposTools
> > > > Loading required package: tools
> > > > [1] "Test:"
> > > > NULL
> > > > Error in getBioC(develOK = TRUE) :
> > > > default: targets affy, cdna and exprs.
> > > > exprs: packages Biobase, annotate, genefilter,
> > > geneploter, edd,
> > > > ROC, multtest, pamr vsn, and limma.
> > > > affy: packages affy, affydata, annaffy, affyPLM,
> > > makecdfenv,
> > > > and matchprobes plus 'exprs'.
> > > > cdna: packages marray, vsn, plus 'exprs'.
> > > > prog: packages graph, hexbin, externalVector.
> > > > graph: packages graph, Rgraphviz, RBGL
> > > > widgets: packages tkWidgets, widgetTools, DynDoc.
> > > > design: packages daMA and factDesign
> > > > externalData: packages externalVector and rhdf5.
> > > > database: AnnBuilder, SAGElyzer, Rdbi and RdbiPgSQL.
> > > > analyses: packages Biobase, ctc, daMA, edd, factDesign,
> > > > genefilter, geneplotter, globaltest,
> gpls, limma,
> > > > RMAGEML, multtest, pamr, wvalue, ROC,
> siggenes and
> > > > splicegear.
> > > > annotation: packages annotate, AnnBuilder, humanLLMappings
> > > > KEGG, GO, SNPtools, makecdfenv and ontoTools.
> > > > proteomics: packages gpls, PROcess and apComplex.
> > > > arrayCGH: packages aCGH, DNAcopy, repeated, and rmutil.
> > > > all: All of the Bio
> > > >
> > > >
> > > > Here's my version info:
> > > > > version
> > > > _
> > > > platform i386-pc-mingw32
> > > > arch i386
> > > > os mingw32
> > > > system i386, mingw32
> > > > status
> > > > major 2
> > > > minor 0.0
> > > > year 2004
> > > > month 10
> > > > day 04
> > > > language R
> > > >
> > > > What's wrong?
> > > >
> > > > Kind regards,
> > > >
> > > > Jelle Goeman
> > > >
> > > > http://www.math.leidenuniv.nl/~jgoeman
> > > >
> > > > _______________________________________________
> > > > Bioconductor mailing list
> > > > Bioconductor at stat.math.ethz.ch
> > > > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > >
> > > --
> > > +-------------------------------------------------------------
> > > --------------+
> > > | Robert Gentleman phone : (617) 632-5250
> > > |
> > > | Associate Professor fax: (617) 632-2444
> > > |
> > > | Department of Biostatistics office: M1B20
> > > |
> > > | Harvard School of Public Health email:
> > > rgentlem at jimmy.harvard.edu |
> > > +-------------------------------------------------------------
> > > --------------+
> > >
>
> --
> +-------------------------------------------------------------
> --------------+
> | Robert Gentleman phone : (617) 632-5250
> |
> | Associate Professor fax: (617) 632-2444
> |
> | Department of Biostatistics office: M1B20
> |
> | Harvard School of Public Health email:
> rgentlem at jimmy.harvard.edu |
> +-------------------------------------------------------------
> --------------+
>
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