[Bioc-devel] Problem with getBioC()

Tue, May 24, 2005 3:23 AM

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:

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

Error in library(Biobase) : there is no package called 'Biobase'

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"

[Bioc-devel] Problem with getBioC()

Thread (2 messages)