[Bioc-devel] Problem with getBioC()
Goeman, J.J. (MSTAT)
J.J.Goeman at lumc.nl
Tue May 24 10:23:15 CEST 2005
Hi,
I'm running getBioC() on a newly installed R 2.1.0 on windows.
All works fine, until I come to the following error message:
Error in sprintf(gettext("unable to move temp installation '%d' to '%s'"), :
use format %s for character objects
This terminates the installation. It did not install all packages.
Best,
Jelle
I used today's getBioC, which says it's version 0.7:
## !!! Always change version number when updating this file !!!
VERSION <- "0.7"
Below is the full output:
> source("http://www.bioconductor.org/getBioC.R")
> getBioC()
Running getBioC version 0.7 with R version 2.1.0
Running biocinstall version 1.0 with R version 2.1.0
also installing the dependencies 'GO', 'KEGG', 'golubEsets', 'RColorBrewer'
trying URL 'http://www.bioconductor.org/packages/data/annotation/stable/bin/windows/contrib/2.1/GO_1.8.2.zip'
Content type 'application/zip' length 12676072 bytes
opened URL
downloaded 12378Kb
trying URL 'http://www.bioconductor.org/packages/data/annotation/stable/bin/windows/contrib/2.1/KEGG_1.8.1.zip'
Content type 'application/zip' length 233148 bytes
opened URL
downloaded 227Kb
trying URL 'http://www.bioconductor.org/packages/data/experiment/stable/bin/windows/contrib/2.1/golubEsets_1.0.zip'
Content type 'application/zip' length 2168986 bytes
opened URL
downloaded 2118Kb
trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.1/RColorBrewer_0.2-3.zip'
Content type 'application/zip' length 45201 bytes
opened URL
downloaded 44Kb
trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/affy_1.6.7.zip'
Content type 'application/zip' length 1438528 bytes
opened URL
downloaded 1404Kb
trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/affydata_1.4.1.zip'
Content type 'application/zip' length 9867339 bytes
opened URL
downloaded 9636Kb
trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/affyPLM_1.3.3.zip'
Content type 'application/zip' length 3912506 bytes
opened URL
downloaded 3820Kb
trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/annaffy_1.0.18.zip'
Content type 'application/zip' length 344446 bytes
opened URL
downloaded 336Kb
trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/annotate_1.5.15.zip'
Content type 'application/zip' length 1673762 bytes
opened URL
downloaded 1634Kb
trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/Biobase_1.5.12.zip'
Content type 'application/zip' length 623915 bytes
opened URL
downloaded 609Kb
trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/Biostrings_1.1.1.zip'
Content type 'application/zip' length 217247 bytes
opened URL
downloaded 212Kb
trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/DynDoc_1.5.5.zip'
Content type 'application/zip' length 91752 bytes
opened URL
downloaded 89Kb
trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/edd_1.5.1.zip'
Content type 'application/zip' length 320107 bytes
opened URL
downloaded 312Kb
trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/gcrma_1.1.3.zip'
Content type 'application/zip' length 131902 bytes
opened URL
downloaded 128Kb
trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/genefilter_1.6.1.zip'
Content type 'application/zip' length 331172 bytes
opened URL
downloaded 323Kb
trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/geneplotter_1.6.1.zip'
Content type 'application/zip' length 1537720 bytes
opened URL
downloaded 1501Kb
trying URL 'http://www.bioconductor.org/packages/data/annotation/stable/bin/windows/contrib/2.1/hgu95av2_1.8.4.zip'
Content type 'application/zip' length 5989106 bytes
opened URL
downloaded 5848Kb
trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/limma_1.9.6.zip'
Content type 'application/zip' length 1307326 bytes
opened URL
downloaded 1276Kb
trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/makecdfenv_1.5.1.zip'
Content type 'application/zip' length 3276551 bytes
opened URL
downloaded 3199Kb
trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/marray_1.6.3.zip'
Content type 'application/zip' length 4363269 bytes
opened URL
downloaded 4261Kb
trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/matchprobes_1.0.22.zip'
Content type 'application/zip' length 7337852 bytes
opened URL
downloaded 7165Kb
trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/multtest_1.6.0.zip'
Content type 'application/zip' length 1550864 bytes
opened URL
downloaded 1514Kb
trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.1/pamr_1.25.zip'
Content type 'application/zip' length 1365701 bytes
opened URL
downloaded 1333Kb
trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/reposTools_1.5.19.zip'
Content type 'application/zip' length 628767 bytes
opened URL
downloaded 614Kb
trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/ROC_1.1.1.zip'
Content type 'application/zip' length 133323 bytes
opened URL
downloaded 130Kb
trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/siggenes_1.2.17.zip'
Content type 'application/zip' length 567331 bytes
opened URL
downloaded 554Kb
trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.1/sma_0.5.14.zip'
Content type 'application/zip' length 3073928 bytes
opened URL
downloaded 3001Kb
trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.1/statmod_1.1.0.zip'
Content type 'application/zip' length 165548 bytes
opened URL
downloaded 161Kb
trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/tkWidgets_1.5.23.zip'
Content type 'application/zip' length 540290 bytes
opened URL
downloaded 527Kb
trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/vsn_1.6.3.zip'
Content type 'application/zip' length 1537894 bytes
opened URL
downloaded 1501Kb
trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/widgetTools_1.4.7.zip'
Content type 'application/zip' length 284075 bytes
opened URL
downloaded 277Kb
trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.1/xtable_1.2-5.zip'
Content type 'application/zip' length 65572 bytes
opened URL
downloaded 64Kb
package 'GO' successfully unpacked and MD5 sums checked
package 'KEGG' successfully unpacked and MD5 sums checked
package 'golubEsets' successfully unpacked and MD5 sums checked
package 'RColorBrewer' successfully unpacked and MD5 sums checked
package 'affy' successfully unpacked and MD5 sums checked
Error in sprintf(gettext("unable to move temp installation '%d' to '%s'"), :
use format %s for character objects
> library(Biobase)
Error in library(Biobase) : there is no package called 'Biobase'
> library(KEGG)
> sessionInfo()
R version 2.1.0, 2005-04-18, i386-pc-mingw32
attached base packages:
[1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" "base"
other attached packages:
KEGG
"1.8.1"
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