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CHECK report for cnvGSA on celaya2

This page was generated on 2019-04-09 13:04:33 -0400 (Tue, 09 Apr 2019).

Package 304/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cnvGSA 1.27.0
Joseph Lugo
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/cnvGSA
Branch: master
Last Commit: 8a73db8
Last Changed Date: 2018-10-30 11:54:30 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: cnvGSA
Version: 1.27.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cnvGSA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cnvGSA_1.27.0.tar.gz
StartedAt: 2019-04-09 00:50:27 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 00:52:42 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 135.1 seconds
RetCode: 0
Status:  OK 
CheckDir: cnvGSA.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cnvGSA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cnvGSA_1.27.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/cnvGSA.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cnvGSA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cnvGSA’ version ‘1.27.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘cnvGSA’ 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
* 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘brglm’ ‘doParallel’ ‘foreach’ ‘splitstackshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
cnvGSAgsTables: no visible global function definition for ‘detectCores’
cnvGSAgsTables: no visible binding for global variable ‘SID’
cnvGSAgsTables: no visible binding for global variable ‘geneID_TYPE’
cnvGSAgsTables: no visible binding for global variable ‘SubjCnvKey’
cnvGSAgsTables: no visible global function definition for
  ‘registerDoParallel’
cnvGSAgsTables: no visible global function definition for ‘%dopar%’
cnvGSAgsTables: no visible global function definition for ‘foreach’
cnvGSAgsTables: no visible binding for global variable ‘i’
cnvGSAgsTables: no visible binding for global variable ‘CHR’
cnvGSAgsTables: no visible binding for global variable ‘BP1’
cnvGSAgsTables: no visible binding for global variable ‘BP2’
cnvGSAgsTables: no visible binding for global variable ‘TYPE’
cnvGSAgsTables: no visible binding for global variable ‘geneID’
cnvGSAgsTables: no visible binding for global variable ‘Symbol’
cnvGSAgsTables: no visible binding for global variable ‘Symbol_TYPE’
cnvGSAgsTables: no visible binding for global variable ‘GsKey’
cnvGSAlogRegTest: no visible binding for global variable ‘GsID’
cnvGSAlogRegTest: no visible binding for global variable ‘GsKey’
cnvGSAlogRegTest: no visible binding for global variable ‘OlpKL_SID’
cnvGSAlogRegTest : f.testGLM_wrap: no visible binding for global
  variable ‘Condition’
cnvGSAlogRegTest : f.testGLM_wrap: no visible global function
  definition for ‘detectCores’
cnvGSAlogRegTest : f.testGLM_wrap: no visible global function
  definition for ‘registerDoParallel’
cnvGSAlogRegTest : f.testGLM_wrap: no visible global function
  definition for ‘%dopar%’
cnvGSAlogRegTest : f.testGLM_wrap: no visible global function
  definition for ‘foreach’
cnvGSAlogRegTest : f.testGLM_wrap: no visible binding for global
  variable ‘i’
cnvGSAlogRegTest : f.testGLM_unit: no visible global function
  definition for ‘glm’
cnvGSAlogRegTest : f.testGLM_unit: no visible global function
  definition for ‘as.formula’
cnvGSAlogRegTest : f.testGLM_unit: no visible global function
  definition for ‘binomial’
cnvGSAlogRegTest : f.testGLM_unit: no visible binding for global
  variable ‘logit’
cnvGSAlogRegTest : f.testGLM_unit: no visible global function
  definition for ‘anova’
cnvGSAlogRegTest: no visible global function definition for ‘p.adjust’
cnvGSAlogRegTest: no visible global function definition for
  ‘write.table’
f.enrProcess: no visible global function definition for ‘write.table’
f.makeViz: no visible global function definition for ‘write.table’
f.makeViz: no visible global function definition for ‘pdf’
f.makeViz: no visible global function definition for ‘par’
f.makeViz: no visible global function definition for ‘barplot’
f.makeViz: no visible global function definition for ‘dev.off’
f.readConfig: no visible global function definition for ‘read.table’
f.readData: no visible global function definition for ‘read.table’
f.readData: no visible binding for global variable ‘IID’
f.readData: no visible binding for global variable ‘FID’
f.readData: no visible binding for global variable ‘AFF’
f.readData: no visible binding for global variable ‘SID’
f.readData: no visible binding for global variable ‘gs_all.ls’
f.readData: no visible binding for global variable ‘gsid2name.chv’
f.readData: no visible global function definition for ‘GRanges’
f.readData: no visible global function definition for ‘Rle’
f.readData: no visible global function definition for ‘IRanges’
f.readData: no visible global function definition for ‘strand’
f.readData: no visible global function definition for ‘start’
f.readData: no visible global function definition for ‘ranges’
f.readData: no visible global function definition for ‘end’
f.readData: no visible global function definition for ‘mcols’
f.readData: no visible binding for global variable ‘OlpKL_CNV’
f.readData: no visible global function definition for ‘stack’
f.readData: no visible binding for global variable ‘geneID_type’
f.readData: no visible binding for global variable ‘CnvKey’
f.readData: no visible binding for global variable ‘OlpKL_SID’
f.readData: no visible binding for global variable ‘geneID_TYPE’
f.readData: no visible binding for global variable ‘SubjCnvKey’
f.readData: no visible binding for global variable ‘GsKey’
f.readData: no visible binding for global variable ‘GsID’
f.readData: no visible binding for global variable ‘GsName’
f.readData: no visible global function definition for ‘cSplit’
f.readData: no visible binding for global variable ‘Symbol’
f.readData: no visible global function definition for ‘aggregate’
Undefined global functions or variables:
  %dopar% AFF BP1 BP2 CHR CnvKey Condition FID GRanges GsID GsKey
  GsName IID IRanges OlpKL_CNV OlpKL_SID Rle SID SubjCnvKey Symbol
  Symbol_TYPE TYPE aggregate anova as.formula barplot binomial cSplit
  detectCores dev.off end foreach geneID geneID_TYPE geneID_type glm
  gs_all.ls gsid2name.chv i logit mcols p.adjust par pdf ranges
  read.table registerDoParallel stack start strand write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "barplot", "par")
  importFrom("stats", "aggregate", "anova", "as.formula", "binomial",
             "end", "glm", "p.adjust", "start")
  importFrom("utils", "read.table", "stack", "write.table")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/cnvGSA.Rcheck/00check.log’
for details.



Installation output

cnvGSA.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL cnvGSA
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘cnvGSA’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘cnvGSA-vignette.Rnw’ 
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cnvGSA)

Tests output


Example timings

cnvGSA.Rcheck/cnvGSA-Ex.timings

nameusersystemelapsed
CnvGSAInput-class0.0000.0000.001
CnvGSAOutput-class0.0000.0000.001
cnvGSAIn0.7110.0280.759
cnvGSAgsTables0.6860.0230.712
cnvGSAlogRegTest0.6700.0140.685
f.enrFiles0.0000.0000.001
f.makeViz0.0000.0000.001
f.readConfig0.7020.0140.717