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CHECK report for sRAP on merida2

This page was generated on 2018-10-17 08:52:10 -0400 (Wed, 17 Oct 2018).

Package 1424/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sRAP 1.20.0
Charles Warden
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/sRAP
Branch: RELEASE_3_7
Last Commit: bae5072
Last Changed Date: 2018-04-30 10:35:31 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: sRAP
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:sRAP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings sRAP_1.20.0.tar.gz
StartedAt: 2018-10-17 00:15:22 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 00:18:32 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 190.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: sRAP.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:sRAP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings sRAP_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/sRAP.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sRAP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sRAP’ version ‘1.20.0’
* 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 ‘sRAP’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
RNA.bdfunc.fc: no visible global function definition for ‘data’
RNA.bdfunc.fc: no visible binding for global variable
  ‘bdfunc.enrichment.human’
RNA.bdfunc.fc: no visible binding for global variable
  ‘bdfunc.enrichment.mouse’
RNA.bdfunc.fc: no visible global function definition for ‘read.table’
RNA.bdfunc.fc: no visible global function definition for ‘pdf’
RNA.bdfunc.fc: no visible global function definition for ‘density’
RNA.bdfunc.fc: no visible global function definition for ‘lines’
RNA.bdfunc.fc: no visible global function definition for ‘legend’
RNA.bdfunc.fc: no visible global function definition for ‘dev.off’
RNA.bdfunc.fc: no visible global function definition for ‘p.adjust’
RNA.bdfunc.fc: no visible global function definition for ‘write.table’
RNA.bdfunc.signal: no visible global function definition for ‘colors’
RNA.bdfunc.signal: no visible global function definition for
  ‘read.table’
RNA.bdfunc.signal: no visible global function definition for ‘data’
RNA.bdfunc.signal: no visible binding for global variable
  ‘bdfunc.enrichment.human’
RNA.bdfunc.signal: no visible binding for global variable
  ‘bdfunc.enrichment.mouse’
RNA.bdfunc.signal: no visible global function definition for ‘aov’
RNA.bdfunc.signal: no visible global function definition for ‘median’
RNA.bdfunc.signal: no visible global function definition for ‘pdf’
RNA.bdfunc.signal: no visible global function definition for ‘boxplot’
RNA.bdfunc.signal: no visible global function definition for ‘dev.off’
RNA.bdfunc.signal: no visible global function definition for ‘slot’
RNA.bdfunc.signal: no visible global function definition for ‘p.adjust’
RNA.bdfunc.signal: no visible global function definition for
  ‘write.table’
RNA.deg: no visible global function definition for ‘colors’
RNA.deg: no visible global function definition for ‘read.table’
RNA.deg: no visible global function definition for ‘p.adjust’
RNA.deg: no visible global function definition for ‘na.omit’
RNA.deg: no visible global function definition for ‘pdf’
RNA.deg: no visible global function definition for ‘boxplot’
RNA.deg: no visible global function definition for ‘dev.off’
RNA.norm: no visible global function definition for ‘read.table’
RNA.qc: no visible global function definition for ‘colors’
RNA.qc: no visible global function definition for ‘read.table’
RNA.qc: no visible global function definition for ‘pdf’
RNA.qc: no visible global function definition for ‘quantile’
RNA.qc: no visible global function definition for ‘density’
RNA.qc: no visible global function definition for ‘legend’
RNA.qc: no visible global function definition for ‘lines’
RNA.qc: no visible global function definition for ‘dev.off’
RNA.qc: no visible global function definition for ‘write.table’
RNA.qc: no visible global function definition for ‘dist’
RNA.qc: no visible global function definition for ‘hclust’
RNA.qc: no visible global function definition for ‘as.dendrogram’
RNA.qc: no visible global function definition for ‘dendrapply’
RNA.qc: no visible global function definition for ‘par’
RNA.qc: no visible global function definition for ‘boxplot’
RNA.qc: no visible global function definition for ‘prcomp’
RNA.qc: no visible global function definition for ‘na.omit’
annova.pvalue: no visible global function definition for ‘aov’
colLab: no visible global function definition for ‘is.leaf’
ks.est: no visible global function definition for ‘ks.test’
ks.pvalue: no visible global function definition for ‘ks.test’
lm.annova.pvalue: no visible global function definition for ‘lm’
lm.annova.pvalue: no visible global function definition for ‘anova’
mwu.est: no visible global function definition for ‘wilcox.test’
mwu.pvalue: no visible global function definition for ‘wilcox.test’
ttest.est: no visible global function definition for ‘t.test’
ttest.pvalue: no visible global function definition for ‘t.test’
Undefined global functions or variables:
  anova aov as.dendrogram bdfunc.enrichment.human
  bdfunc.enrichment.mouse boxplot colors data dendrapply density
  dev.off dist hclust is.leaf ks.test legend lines lm median na.omit
  p.adjust par pdf prcomp quantile read.table slot t.test wilcox.test
  write.table
Consider adding
  importFrom("grDevices", "colors", "dev.off", "pdf")
  importFrom("graphics", "boxplot", "legend", "lines", "par")
  importFrom("methods", "slot")
  importFrom("stats", "anova", "aov", "as.dendrogram", "dendrapply",
             "density", "dist", "hclust", "is.leaf", "ks.test", "lm",
             "median", "na.omit", "p.adjust", "prcomp", "quantile",
             "t.test", "wilcox.test")
  importFrom("utils", "data", "read.table", "write.table")
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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                              old_size new_size compress
  bdfunc.enrichment.human.rda    1.3Mb    951Kb    bzip2
  bdfunc.enrichment.mouse.rda     31Kb     26Kb       xz
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
RNA.bdfunc.signal 106.305  0.662 108.452
RNA.bdfunc.fc      18.029  0.417  18.775
RNA.deg            15.677  0.398  16.319
* 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/sRAP.Rcheck/00check.log’
for details.



Installation output

sRAP.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL sRAP
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘sRAP’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (sRAP)

Tests output


Example timings

sRAP.Rcheck/sRAP-Ex.timings

nameusersystemelapsed
RNA.bdfunc.fc18.029 0.41718.775
RNA.bdfunc.signal106.305 0.662108.452
RNA.deg15.677 0.39816.319
RNA.norm3.4090.1093.581
RNA.prepare.input0.0250.0130.043
RNA.qc3.5470.1123.705