[Bioc-devel] Problem with getBioC()

[Goeman, J.J. (MSTAT)]

 Hi Robert,

> so use options(error=recover)
> 
> select the frame for sprintf and then see what tmpDir, curPkg and 
> instPath are, one suspects that therein lies the problem

I've tried this on a new installation of R. This time it breaks down at annaffy.

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
package 'affydata' successfully unpacked and MD5 sums checked
package 'affyPLM' successfully unpacked and MD5 sums checked
package 'annaffy' successfully unpacked and MD5 sums checked
Error in sprintf(gettext("unable to move temp installation '%d' to '%s'"),  : 
        use format %s for character objects

Enter a frame number, or 0 to exit   

1: getBioC()
2: do.call("biocinstall", args)
3: biocinstall(lib = "C:/R/rw2010/library", groupName = "default", dependencies = c
4: do.call("install.packages", args)
5: install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy", "annotate", 
6: .install.winbinary(pkgs = pkgs, lib = lib, contriburl = contriburl, method = met
7: unpackPkg(foundpkgs[okp, 2], foundpkgs[okp, 1], lib, installWithVers)
8: warning(sprintf(gettext("unable to move temp installation '%d' to '%s'"), file.p
9: sprintf(gettext("unable to move temp installation '%d' to '%s'"), file.path(tmpD

Selection: 9
Called from: eval(expr, envir, enclos)
Browse[1]>  tmpDir
Error during wrapup: Object "tmpDir" not found
Browse[1]> curPkg
Error during wrapup: Object "curPkg" not found
Browse[1]> instPath
Error during wrapup: Object "instPath" not found
 
The same at selection 8. At selection 7 I get:

Selection: 7
Called from: eval(expr, envir, enclos)
Browse[1]> instPath
[1] "C:/R/rw2010/library/annaffy"
Browse[1]>  tmpDir
[1] "C:/R/rw2010/library\\file13987"
Browse[1]> curPkg
[1] "annaffy"
Browse[1]> file.path(tmpDir, curPkg)
[1] "C:/R/rw2010/library\\file13987/annaffy"
Browse[1]> sprintf(gettext("unable to move temp installation '%d' to '%s'"), 
+        file.path(tmpDir, curPkg), instPath)
Error during wrapup: use format %s for character objects
Browse[1]> class(file.path(tmpDir, curPkg))
[1] "character"

The "use format %s for character objects" is the reported error that getBioC() breaks down on. This should be repaired with changing %d to %s:

Browse[1]> sprintf(gettext("unable to move temp installation '%s' to '%s'"), 
+         file.path(tmpDir, curPkg), instPath)
[1] "unable to move temp installation 'C:/R/rw2010/library\\file13987/annaffy' to 'C:/R/rw2010/library/annaffy'"

I still don't know what this warning comes from. The folder 'C:/R/rw2010/library\\file13987/annaffy' neatly contains the affy package. The folder 'C:/R/rw2010/library/annaffy' does not exist yet. 

Best,

Jelle


Full traceback again below:

9: sprintf(gettext("unable to move temp installation '%d' to '%s'"), 
       file.path(tmpDir, curPkg), instPath)
8: warning(sprintf(gettext("unable to move temp installation '%d' to '%s'"), 
       file.path(tmpDir, curPkg), instPath), domain = NA, call. = FALSE)
7: unpackPkg(foundpkgs[okp, 2], foundpkgs[okp, 1], lib, installWithVers)
6: .install.winbinary(pkgs = pkgs, lib = lib, contriburl = contriburl, 
       method = method, available = available, destdir = destdir, 
       installWithVers = installWithVers, dependencies = dependencies)
5: install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy", 
   "annotate", "Biobase", "Biostrings", "DynDoc", "edd", "gcrma", 
   "genefilter", "geneplotter", "hgu95av2", "limma", "makecdfenv", 
   "marray", "matchprobes", "multtest", "pamr", "reposTools", "ROC", 
   "siggenes", "sma", "statmod", "tkWidgets", "vsn", "widgetTools", 
   "xtable"), repos = c("http://www.bioconductor.org/packages/bioc/stable", 
   "http://www.bioconductor.org/packages/data/annotation/stable", 
   "http://www.bioconductor.org/packages/data/experiment/stable", 
   "http://www.bioconductor.org/packages/omegahat/stable", "http://www.bioconductor.org/packages/lindsey/stable", 
   "http://cran.fhcrc.org"), lib = "C:/PROGRA~1/R/rw2010/library", 
       dependencies = c("Depends", "Imports"))
4: do.call("install.packages", args)
3: biocinstall(lib = "C:/PROGRA~1/R/rw2010/library", groupName = "default", 
       dependencies = c("Depends", "Imports"))
2: do.call("biocinstall", args)
1: getBioC()