BioC 2.12: CHECK report for sigaR on moscato2

Package: sigaR

Version: 1.3.2

Command: rm -rf sigaR.buildbin-libdir && mkdir sigaR.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=sigaR.buildbin-libdir sigaR_1.3.2.tar.gz >sigaR-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=sigaR.buildbin-libdir --install="check:sigaR-install.out" --force-multiarch --no-vignettes --timings sigaR_1.3.2.tar.gz && mv sigaR.buildbin-libdir/* sigaR.Rcheck/ && rmdir sigaR.buildbin-libdir

StartedAt: 2013-03-25 04:52:43 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 05:01:24 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 520.9 seconds

RetCode: 0

Status: OK

CheckDir: sigaR.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/sigaR.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 'sigaR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sigaR' version '1.3.2'
* 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 'sigaR' 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
ExpressionSet2weightedSubset: no visible binding for global variable
  'sigaR'
RCMestimation : RCMmlH2: multiple local function definitions for
  'tau.estimator' with different formal arguments
RCMtest: no visible binding for global variable 'sigaR'
RCMtest: no visible binding for global variable 'quadprog'
RCMtest: no visible binding for global variable 'MASS'
cghCall2maximumSubset: no visible binding for global variable 'sigaR'
cghCall2weightedSubset: no visible binding for global variable 'sigaR'
cghSeg2weightedSubset: no visible binding for global variable 'sigaR'
entropyTest: no visible binding for global variable 'sigaR'
entropyTest: no visible binding for global variable 'corpcor'
matchAnn2Ann: no visible binding for global variable 'sigaR'
matchCGHcall2ExpressionSet: no visible binding for global variable
  'sigaR'
mutInfTest: no visible binding for global variable 'sigaR'
mutInfTest: no visible binding for global variable 'corpcor'
* 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 ... NOTE
  '.find.package' is deprecated.
  Use 'find.package' instead.
  See help("Deprecated")
  '.find.package' is deprecated.
  Use 'find.package' instead.
  See help("Deprecated")
  '.find.package' is deprecated.
  Use 'find.package' instead.
  See help("Deprecated")
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... [207s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
mutInfTest    162.22   4.59  166.82
cisEffectTune  17.30   0.00   17.32
** running examples for arch 'x64' ... [221s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
mutInfTest    172.21   5.09  177.31
cisEffectTune  19.47   0.00   19.47
RCMtest         5.75   0.00    5.74
* 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 were 2 notes.
See
  'E:/biocbld/bbs-2.12-bioc/meat/sigaR.Rcheck/00check.log'
for details.


install for i386

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

install for x64

* installing *source* package 'sigaR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sigaR' as sigaR_1.3.2.zip
* DONE (sigaR)

Summary

Command output