BioC 2.12: CHECK report for GGBase on moscato2

Package: GGBase

Version: 3.22.0

Command: rm -rf GGBase.buildbin-libdir && mkdir GGBase.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GGBase.buildbin-libdir GGBase_3.22.0.tar.gz >GGBase-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=GGBase.buildbin-libdir --install="check:GGBase-install.out" --force-multiarch --no-vignettes --timings GGBase_3.22.0.tar.gz && mv GGBase.buildbin-libdir/* GGBase.Rcheck/ && rmdir GGBase.buildbin-libdir

StartedAt: 2013-10-09 02:19:22 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 02:26:51 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 448.4 seconds

RetCode: 0

Status:  OK

CheckDir: GGBase.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/GGBase.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GGBase/DESCRIPTION' ... OK
* this is package 'GGBase' version '3.22.0'
* 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 'GGBase' can be installed ... OK
* checking installed package size ... OK
* checking package 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.oldcode : <anonymous>: warning in axis(3, at = genePosition(x@gene,
  annlib = x@annotation), col = "red", lwd = 2, label = " "): partial
  argument match of 'label' to 'labels'
.oldcode : pedinf2df: warning in read.table(fn, h = FALSE): partial
  argument match of 'h' to 'header'
allsnps: warning in dir(system.file("parts", package = packname), full
  = TRUE): partial argument match of 'full' to 'full.names'
.oldcode : genePosition: no visible global function definition for
  'revmap'
.oldcode : featureFilter: no visible global function definition for
  'keys'
.oldcode : sym2pid: no visible global function definition for 'revmap'
.oldcode : <anonymous>: no visible global function definition for
  'revmap'
.oldcode : snpLocs.Hsapiens: no visible global function definition for
  'getSNPlocs'
sym2pid: no visible global function definition for 'revmap'
plot_EvG,genesym-rsid-smlSet: no visible global function definition for
  'revmap'
* 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 installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... [31s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
MAFfilter   7.79   0.42    8.93
make_smlSet 5.72   0.18    5.89
plot_EvG    5.25   0.21    5.55
** running examples for arch 'x64' ... [34s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
MAFfilter   8.36   0.56    8.93
make_smlSet 5.66   0.22    5.91
plot_EvG    5.39   0.20    5.98
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'MAFfilter.R' [15s]
  Running 'make.R' [17s]
  Running 'plot_EvG.R' [18s]
 [51s] OK
** running tests for arch 'x64'
  Running 'MAFfilter.R' [19s]
  Running 'make.R' [20s]
  Running 'plot_EvG.R' [22s]
 [62s] OK
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  'E:/biocbld/bbs-2.12-bioc/meat/GGBase.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'GGBase' ...
** R
** 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 'GGBase' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GGBase' as GGBase_3.22.0.zip
* DONE (GGBase)