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CHECK report for MergeMaid on malbec1

This page was generated on 2019-04-16 11:47:56 -0400 (Tue, 16 Apr 2019).

Package 908/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MergeMaid 2.54.0
Xiaogang Zhong
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/MergeMaid
Branch: RELEASE_3_8
Last Commit: 8e79bd2
Last Changed Date: 2018-10-30 11:41:41 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: MergeMaid
Version: 2.54.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:MergeMaid.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings MergeMaid_2.54.0.tar.gz
StartedAt: 2019-04-16 01:13:30 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:15:10 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 99.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: MergeMaid.Rcheck
Warnings: 1

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:MergeMaid.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings MergeMaid_2.54.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/MergeMaid.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MergeMaid/DESCRIPTION’ ... OK
* this is package ‘MergeMaid’ version ‘2.54.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
intcorDens               17.560  0.064  17.640
class.mergeExpressionSet  9.436  0.052   9.499
intCor                    7.688  0.004   7.697
class.mergeCor            5.928  0.012   5.943
* 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/MergeMaid.Rcheck/00check.log’
for details.



Installation output

MergeMaid.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL MergeMaid
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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.mergeCoeff1.2040.0041.210
class.mergeCor5.9280.0125.943
class.mergeExpressionSet9.4360.0529.499
intCor7.6880.0047.697
intcorDens17.560 0.06417.640
intersection0.1360.0000.137
mergeExprs4.7280.0044.743
modelOutcome2.5600.0002.566