BioC 2.12: CHECK report for a4Base on moscato2

Package: a4Base

Version: 1.7.1

Command: rm -rf a4Base.buildbin-libdir && mkdir a4Base.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=a4Base.buildbin-libdir a4Base_1.7.1.tar.gz >a4Base-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=a4Base.buildbin-libdir --install="check:a4Base-install.out" --force-multiarch --no-vignettes --timings a4Base_1.7.1.tar.gz && mv a4Base.buildbin-libdir/* a4Base.Rcheck/ && rmdir a4Base.buildbin-libdir

StartedAt: 2013-03-25 00:42:09 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:49:09 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 420.7 seconds

RetCode: 0

Status: WARNINGS

CheckDir: a4Base.Rcheck

Warnings: 1

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/a4Base.Rcheck'
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'a4Base/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'a4Base' version '1.7.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'gridSVG'
* 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 'a4Base' 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 ... WARNING
Foreign function call with 'PACKAGE' argument in a base package:
  .C("bincode", ..., PACKAGE = "base")
Packages should not make .C/.Call/.Fortran calls to base packages. They
are not part of the API, for use only by R itself and subject to change
without notice.
* checking R code for possible problems ... NOTE
plotLogRatio: no visible global function definition for 'JavaGD'
plotLogRatio: no visible global function definition for 'grid.garnish'
plotLogRatio: no visible global function definition for
  'grid.hyperlink'
plotLogRatio: no visible global function definition for 'grid.script'
plotLogRatio: no visible global function definition for 'gridToSVG'
* 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 examples ...
** running examples for arch 'i386' ... [95s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
spectralMap     18.40   1.12   19.52
computeLogRatio 11.01   0.10   11.10
plotLogRatio     9.37   0.14    9.51
** running examples for arch 'x64' ... [108s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
spectralMap     21.68   1.41   23.12
plotLogRatio    13.46   0.08   13.54
computeLogRatio 12.54   0.10   12.83
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  'E:/biocbld/bbs-2.12-bioc/meat/a4Base.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'a4Base' ...
** R
** data
** inst
** preparing package for lazy loading
'.path.package' is deprecated.
Use 'path.package' instead.
See help("Deprecated")
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
'.path.package' is deprecated.
Use 'path.package' instead.
See help("Deprecated")

install for x64

* installing *source* package 'a4Base' ...
** testing if installed package can be loaded
'.path.package' is deprecated.
Use 'path.package' instead.
See help("Deprecated")
* MD5 sums
packaged installation of 'a4Base' as a4Base_1.7.1.zip
* DONE (a4Base)

Summary

Command output