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

This page was generated on 2015-10-27 17:31:51 -0400 (Tue, 27 Oct 2015).

Package 233/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cpvSNP 1.2.0
Caitlin McHugh
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/cpvSNP
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: cpvSNP
Version: 1.2.0
Command: rm -rf cpvSNP.buildbin-libdir cpvSNP.Rcheck && mkdir cpvSNP.buildbin-libdir cpvSNP.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cpvSNP.buildbin-libdir cpvSNP_1.2.0.tar.gz >cpvSNP.Rcheck\00install.out 2>&1 && cp cpvSNP.Rcheck\00install.out cpvSNP-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=cpvSNP.buildbin-libdir --install="check:cpvSNP-install.out" --force-multiarch --no-vignettes --timings cpvSNP_1.2.0.tar.gz
StartedAt: 2015-10-27 01:00:05 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 01:12:04 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 718.8 seconds
RetCode: 0
Status:  OK  
CheckDir: cpvSNP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf cpvSNP.buildbin-libdir cpvSNP.Rcheck && mkdir cpvSNP.buildbin-libdir cpvSNP.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cpvSNP.buildbin-libdir cpvSNP_1.2.0.tar.gz >cpvSNP.Rcheck\00install.out 2>&1 && cp cpvSNP.Rcheck\00install.out cpvSNP-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=cpvSNP.buildbin-libdir --install="check:cpvSNP-install.out" --force-multiarch --no-vignettes --timings cpvSNP_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/cpvSNP.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 'cpvSNP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cpvSNP' version '1.2.0'
* 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' ... [122s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
geneToSNPList 2.56   0.18  115.17
** running examples for arch 'x64' ... [133s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
geneToSNPList 2.37    0.2  124.63
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [112s]
 [112s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [133s]
 [133s] 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
  'C:/biocbld/bbs-3.2-bioc/meat/cpvSNP.Rcheck/00check.log'
for details.


cpvSNP.Rcheck/00install.out:


install for i386

* installing *source* package 'cpvSNP' ...
** 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 'cpvSNP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cpvSNP' as cpvSNP_1.2.0.zip
* DONE (cpvSNP)

cpvSNP.Rcheck/examples_i386/cpvSNP-Ex.timings:

nameusersystemelapsed
GLOSSIResult-class000
GLOSSIResultCollection-class000
GeneSetResult-class000
GeneSetResultCollection-class000
VEGASResult-class000
VEGASResultCollection-class000
createArrayData0.220.000.22
degreesOfFreedom-method000
geneSetAnalysis0.170.000.17
geneSetName-methods000
geneToSNPList 2.56 0.18115.17
glossi000
glossiMarginal0.010.000.01
pValue-method000
simulatedStats-method000
statistic-methods000

cpvSNP.Rcheck/examples_x64/cpvSNP-Ex.timings:

nameusersystemelapsed
GLOSSIResult-class000
GLOSSIResultCollection-class000
GeneSetResult-class000
GeneSetResultCollection-class000
VEGASResult-class0.010.000.01
VEGASResultCollection-class000
createArrayData0.210.000.21
degreesOfFreedom-method000
geneSetAnalysis0.20.00.2
geneSetName-methods000
geneToSNPList 2.37 0.20124.63
glossi0.020.000.01
glossiMarginal000
pValue-method000
simulatedStats-method0.010.000.01
statistic-methods000