BioC 3.2: CHECK report for gage on windows1.bioconductor.org

Package: gage

Version: 2.20.0

Command: rm -rf gage.buildbin-libdir gage.Rcheck && mkdir gage.buildbin-libdir gage.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gage.buildbin-libdir gage_2.20.0.tar.gz >gage.Rcheck\00install.out 2>&1 && cp gage.Rcheck\00install.out gage-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=gage.buildbin-libdir --install="check:gage-install.out" --force-multiarch --no-vignettes --timings gage_2.20.0.tar.gz

StartedAt: 2015-10-27 01:51:47 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 01:54:10 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 143.5 seconds

RetCode: 1

Status:  ERROR

CheckDir: gage.Rcheck

Warnings: NA

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### Running command:
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###   rm -rf gage.buildbin-libdir gage.Rcheck && mkdir gage.buildbin-libdir gage.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gage.buildbin-libdir gage_2.20.0.tar.gz >gage.Rcheck\00install.out 2>&1 && cp gage.Rcheck\00install.out gage-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=gage.buildbin-libdir --install="check:gage-install.out" --force-multiarch --no-vignettes --timings gage_2.20.0.tar.gz
###
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/gage.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'gage/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gage' version '2.20.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'gage' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'GO.db' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
deComp: no visible global function definition for 'annot.db'
eg2sym: no visible binding for global variable 'egSymb'
esset.grp: no visible global function definition for 'nodes'
esset.grp: no visible global function definition for 'edgeNames'
esset.grp: no visible global function definition for 'make.graph'
esset.grp : <anonymous>: no visible global function definition for
  'nodes'
go.gsets: no visible global function definition for 'biocLite'
go.gsets: no visible binding for global variable 'GOTERM'
kegg.gsets: no visible binding for global variable 'khier'
kegg.species.code: no visible binding for global variable 'korg'
sym2eg: no visible binding for global variable 'egSymb'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'gage-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: kegg.gsets
> ### Title: Generate up-to-date KEGG pathway gene sets
> ### Aliases: kegg.gsets
> ### Keywords: ˜kwd1 ˜kwd2
> 
> ### ** Examples
> 
> #GAGE analysis use the latest KEGG pathway  definitions, instead of
> #kegg.gs
> kg.hsa=kegg.gsets()
> data(gse16873)
> hn=(1:6)*2-1
> dcis=(1:6)*2
> kegg.sigmet=kg.hsa$kg.sets[kg.hsa$sigmet.idx]
> gse16873.kegg.p <- gage(gse16873, gsets = kegg.sigmet,
+                         ref = hn, samp = dcis)
> 
> #E coli KEGG Id is different from Entre Gene
> kg.eco=kegg.gsets("eco")
Error in FUN(X[[i]], ...) : subscript out of bounds
Calls: kegg.gsets ... .getUrl -> do.call -> <Anonymous> -> sapply -> lapply
Execution halted
** running examples for arch 'x64' ... [25s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
kegg.gsets 0.78      0    10.1
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  'C:/biocbld/bbs-3.2-bioc/meat/gage.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'gage' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'gage' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gage' as gage_2.20.0.zip
* DONE (gage)

name	user	system	elapsed
eg2sym	1.10	0.01	1.11
egSymb	0.90	0.02	0.92
essGene	0.29	0.00	0.28
esset.grp	1.14	0.02	1.16
gage	1.70	0.06	1.76
gageComp	0.80	0.00	0.86
gagePipe	0.67	0.01	0.69
geneData	0.29	0.05	0.34
go.gsets	0	0	0
gs.tTest	0.16	0.00	0.15
gse16873	0.40	0.02	0.43
heter.gage	0.42	0.00	0.42
kegg.gs	0.84	0.00	0.85

name	user	system	elapsed
eg2sym	1.61	0.09	1.70
egSymb	1.05	0.08	1.12
essGene	0.45	0.01	0.47
esset.grp	1.3	0.0	1.3
gage	1.87	0.04	1.91
gageComp	1.11	0.01	1.12
gagePipe	0.89	0.03	0.92
geneData	0.43	0.00	0.42
go.gsets	0	0	0
gs.tTest	0.15	0.03	0.19
gse16873	0.24	0.00	0.24
heter.gage	0.65	0.00	0.65
kegg.gs	0.93	0.00	0.92
kegg.gsets	0.78	0.00	10.10
readExpData	0	0	0
readList	0.14	0.00	0.14
sigGeneSet	0.42	0.02	0.44