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CHECK report for MergeMaid on merida2

This page was generated on 2018-10-17 08:46:21 -0400 (Wed, 17 Oct 2018).

Package 859/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MergeMaid 2.52.0
Xiaogang Zhong
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/MergeMaid
Branch: RELEASE_3_7
Last Commit: 88a1ddf
Last Changed Date: 2018-04-30 10:35:00 -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: MergeMaid
Version: 2.52.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MergeMaid.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MergeMaid_2.52.0.tar.gz
StartedAt: 2018-10-16 22:27:32 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 22:29:29 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 117.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: MergeMaid.Rcheck
Warnings: 1

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:MergeMaid.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MergeMaid_2.52.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/MergeMaid.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 ‘MergeMaid/DESCRIPTION’ ... OK
* this is package ‘MergeMaid’ version ‘2.52.0’
* 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 ‘MergeMaid’ 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:
  ‘MASS’ ‘methods’ ‘survival’
  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
.dens.mergeExpressionSet: no visible global function definition for
  ‘density’
.fdr.mergeCor: no visible global function definition for ‘.getnull’
.fdr.mergeCor: no visible global function definition for ‘approxfun’
.fdr.mergeCor: no visible global function definition for ‘density’
.fdr.mergeCor: no visible global function definition for ‘integrate’
.ic.plot : norm: no visible global function definition for ‘sd’
.ic.plot: no visible global function definition for ‘cov’
.icor : norm: no visible global function definition for ‘sd’
.icor: no visible global function definition for ‘cov’
.intcor : norm: no visible global function definition for ‘sd’
.intcor: no visible global function definition for ‘new’
.integ.cal : sziicor: no visible global function definition for ‘cor’
.mergemodel: no visible global function definition for ‘lm’
.mergemodel: no visible binding for global variable ‘na.omit’
.mergemodel: no visible global function definition for ‘coxph’
.mergemodel: no visible global function definition for ‘sd’
.mergemodel: no visible global function definition for ‘glm’
.mergemodel: no visible binding for global variable ‘binomial’
.model.outcome: no visible global function definition for ‘new’
.nullicornorm : norm: no visible global function definition for ‘sd’
.nullicornorm: no visible global function definition for ‘cov’
.nullicornorm : getone: no visible global function definition for
  ‘rnorm’
maxintcor: no visible global function definition for ‘cov’
maxintcor: no visible global function definition for ‘ginv’
mergeExprs: no visible global function definition for ‘new’
mergeget: no visible global function definition for ‘new’
subsetmES: no visible global function definition for ‘new’
intersection,mergeExpressionSet: no visible global function definition
  for ‘new’
Undefined global functions or variables:
  .getnull approxfun binomial cor cov coxph density ginv glm integrate
  lm na.omit new rnorm sd
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "approxfun", "binomial", "cor", "cov", "density",
             "glm", "integrate", "lm", "na.omit", "rnorm", "sd")
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 ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'mergeExpressionSet,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 or elapsed time > 5s
                           user system elapsed
intcorDens               22.034  0.281  22.499
class.mergeExpressionSet 11.152  0.124  11.393
intCor                    7.591  0.069   7.717
class.mergeCor            6.617  0.039   6.727
mergeExprs                5.086  0.071   5.202
* 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-3.7-bioc/meat/MergeMaid.Rcheck/00check.log’
for details.



Installation output

MergeMaid.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MergeMaid
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘MergeMaid’ ...
** R
** data
** 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 (MergeMaid)

Tests output


Example timings

MergeMaid.Rcheck/MergeMaid-Ex.timings

nameusersystemelapsed
class.mergeCoeff1.5190.0451.581
class.mergeCor6.6170.0396.727
class.mergeExpressionSet11.152 0.12411.393
intCor7.5910.0697.717
intcorDens22.034 0.28122.499
intersection0.1160.0090.127
mergeExprs5.0860.0715.202
modelOutcome1.8150.0231.856