Package: GeneExpressionSignature

Version: 1.33.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneExpressionSignature.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneExpressionSignature_1.33.0.tar.gz

StartedAt: 2020-01-16 04:43:43 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 04:46:06 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 142.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: GeneExpressionSignature.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneExpressionSignature.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneExpressionSignature_1.33.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/GeneExpressionSignature.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneExpressionSignature/DESCRIPTION’ ... OK
* this is package ‘GeneExpressionSignature’ version ‘1.33.0’
* 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 ‘GeneExpressionSignature’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'KEGG.db' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.11-bioc/meat/GeneExpressionSignature.Rcheck/00install.out’ for details.
* 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:
  ‘Biobase’ ‘PGSEA’
  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
RankMerging: no visible global function definition for ‘exprs’
RankMerging: no visible global function definition for ‘as’
RankMerging: no visible global function definition for ‘phenoData’
RankMerging: no visible global function definition for ‘new’
ScoreGSEA : PRL.Distance: no visible global function definition for
  ‘exprs’
ScoreGSEA: no visible global function definition for ‘exprs’
ScorePGSEA: no visible global function definition for ‘exprs’
ScorePGSEA: no visible global function definition for ‘new’
ScorePGSEA: no visible global function definition for ‘PGSEA’
ScorePGSEA: no visible global function definition for ‘pnorm’
getRLs : Check.Log: no visible global function definition for ‘median’
integratePRL: no visible global function definition for ‘phenoData’
integratePRL: no visible global function definition for ‘exprs’
integratePRL: no visible global function definition for ‘new’
integratePRL: no visible global function definition for ‘as’
Undefined global functions or variables:
  PGSEA as exprs median new phenoData pnorm
Consider adding
  importFrom("methods", "as", "new")
  importFrom("stats", "median", "pnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
ScoreGSEA         5.579  2.108   7.689
SignatureDistance 5.437  1.976   7.414
ScorePGSEA        4.139  1.621   5.761
* 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/GeneExpressionSignature.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GeneExpressionSignature
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘GeneExpressionSignature’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning message:
Package 'KEGG.db' is deprecated and will be removed from Bioconductor
  version 3.12 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'KEGG.db' is deprecated and will be removed from Bioconductor
  version 3.12
** testing if installed package can be loaded from final location
Warning: Package 'KEGG.db' is deprecated and will be removed from Bioconductor
  version 3.12
** testing if installed package keeps a record of temporary installation path
* DONE (GeneExpressionSignature)

name	user	system	elapsed
RankMerging	1.993	0.530	2.523
ScoreGSEA	5.579	2.108	7.689
ScorePGSEA	4.139	1.621	5.761
SignatureDistance	5.437	1.976	7.414
exampleSet	0.372	0.031	0.404
getRLs	1.138	0.122	1.313