BioC 3.1: CHECK report for cpvSNP on moscato2

Package: cpvSNP

Version: 1.0.0

Command: rm -rf cpvSNP.buildbin-libdir cpvSNP.Rcheck && mkdir cpvSNP.buildbin-libdir cpvSNP.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cpvSNP.buildbin-libdir cpvSNP_1.0.0.tar.gz >cpvSNP.Rcheck\00install.out 2>&1 && cp cpvSNP.Rcheck\00install.out cpvSNP-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=cpvSNP.buildbin-libdir --install="check:cpvSNP-install.out" --force-multiarch --no-vignettes --timings cpvSNP_1.0.0.tar.gz

StartedAt: 2015-10-09 00:50:12 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 01:05:17 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 904.9 seconds

RetCode: 0

Status:  OK

CheckDir: cpvSNP.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf cpvSNP.buildbin-libdir cpvSNP.Rcheck && mkdir cpvSNP.buildbin-libdir cpvSNP.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cpvSNP.buildbin-libdir cpvSNP_1.0.0.tar.gz >cpvSNP.Rcheck\00install.out 2>&1 && cp cpvSNP.Rcheck\00install.out cpvSNP-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=cpvSNP.buildbin-libdir --install="check:cpvSNP-install.out" --force-multiarch --no-vignettes --timings cpvSNP_1.0.0.tar.gz
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/cpvSNP.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cpvSNP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cpvSNP' version '1.0.0'
* 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 'cpvSNP' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'GSEABase' which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
createArrayData: no visible global function definition for 'GRanges'
createArrayData: no visible global function definition for 'Rle'
createArrayData: no visible global function definition for 'IRanges'
createArrayData: no visible global function definition for
  'elementMetadata<-'
geneToSNPList: no visible global function definition for 'findOverlaps'
plotPvals: no visible binding for global variable 'pval'
vegasPrep: no visible global function definition for 'elementMetadata'
* 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' ... [148s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
geneToSNPList 7.32   0.14  139.29
** running examples for arch 'x64' ... [170s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
geneToSNPList 9.33   0.23  160.01
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [141s]
 [144s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [173s]
 [173s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/cpvSNP.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'cpvSNP' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'cpvSNP' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'cpvSNP' as cpvSNP_1.0.0.zip
* DONE (cpvSNP)

name	user	system	elapsed
GLOSSIResult-class	0	0	0
GLOSSIResultCollection-class	0	0	0
GeneSetResult-class	0	0	0
GeneSetResultCollection-class	0	0	0
VEGASResult-class	0	0	0
VEGASResultCollection-class	0	0	0
createArrayData	0.28	0.00	0.28
degreesOfFreedom-method	0	0	0
geneSetAnalysis	0.20	0.00	0.21
geneSetName-methods	0	0	0
geneToSNPList	7.32	0.14	139.29
glossi	0.02	0.00	0.01
glossiMarginal	0	0	0
pValue-method	0	0	0
simulatedStats-method	0	0	0
statistic-methods	0	0	0

name	user	system	elapsed
GLOSSIResult-class	0	0	0
GLOSSIResultCollection-class	0.02	0.00	0.02
GeneSetResult-class	0	0	0
GeneSetResultCollection-class	0	0	0
VEGASResult-class	0	0	0
VEGASResultCollection-class	0	0	0
createArrayData	0.31	0.00	0.31
degreesOfFreedom-method	0	0	0
geneSetAnalysis	0.28	0.02	0.29
geneSetName-methods	0	0	0
geneToSNPList	9.33	0.23	160.01
glossi	0.03	0.00	0.03
glossiMarginal	0	0	0
pValue-method	0	0	0
simulatedStats-method	0	0	0
statistic-methods	0	0	0