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CHECK report for compartmap on celaya2

This page was generated on 2020-01-16 13:52:51 -0500 (Thu, 16 Jan 2020).

Package 342/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
compartmap 1.5.0
Benjamin Johnson
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/compartmap
Branch: master
Last Commit: f861a62
Last Changed Date: 2019-10-29 13:43:22 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: compartmap
Version: 1.5.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:compartmap.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings compartmap_1.5.0.tar.gz
StartedAt: 2020-01-16 03:08:57 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 03:19:35 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 638.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: compartmap.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:compartmap.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings compartmap_1.5.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/compartmap.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 ‘compartmap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘compartmap’ version ‘1.5.0’
* package encoding: UTF-8
* 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 ‘compartmap’ 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
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.arraycompartments: no visible global function definition for
  ‘seqlevels’
.createCorMatrix: no visible global function definition for ‘seqlevels’
.createCorMatrix: no visible global function definition for
  ‘seqlevels<-’
.createCorMatrix: no visible global function definition for ‘cor’
.extractAB: no visible global function definition for ‘cor’
.extractAB: no visible global function definition for ‘colSums2’
.fsvd: no visible global function definition for ‘rnorm’
.getFirstPC: no visible global function definition for ‘cor’
.getFirstPCarray: no visible global function definition for ‘rowMeans2’
.getPairedAllChrsArray: no visible global function definition for
  ‘seqlevels’
.removeBadBins: no visible global function definition for ‘colAlls’
.returnBinnedMatrix : bin2D: no visible global function definition for
  ‘median’
.returnBinnedMatrix: no visible global function definition for
  ‘seqlengths’
.returnBinnedMatrix: no visible global function definition for
  ‘standardChromosomes’
.returnBinnedMatrix: no visible global function definition for
  ‘seqlengths<-’
.returnBinnedMatrix: no visible global function definition for
  ‘seqlevels’
.returnBinnedMatrix: no visible global function definition for
  ‘subjectHits’
.run_examples: no visible global function definition for ‘data’
.run_examples: no visible binding for global variable
  ‘bulkATAC_raw_filtered_chr14’
.run_examples: no visible binding for global variable
  ‘filtered.data.chr14’
.run_examples: no visible binding for global variable
  ‘meth_array_450k_chr14’
.run_examples: no visible binding for global variable
  ‘array.data.chr14’
.unitarize: no visible global function definition for ‘median’
getBinMatrix: no visible global function definition for ‘seqlengths’
getBinMatrix: no visible global function definition for ‘IRanges’
getCompartments: no visible global function definition for ‘seqlevels’
getCorMatrix: no visible global function definition for ‘cor’
plotAB: no visible global function definition for ‘barplot’
Undefined global functions or variables:
  IRanges array.data.chr14 barplot bulkATAC_raw_filtered_chr14 colAlls
  colSums2 cor data filtered.data.chr14 median meth_array_450k_chr14
  rnorm rowMeans2 seqlengths seqlengths<- seqlevels seqlevels<-
  standardChromosomes subjectHits
Consider adding
  importFrom("graphics", "barplot")
  importFrom("stats", "cor", "median", "rnorm")
  importFrom("utils", "data")
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 ... WARNING
Codoc mismatches from documentation object 'getABSignal':
getABSignal
  Code: function(x, k = 2, iter = 2, squeeze = FALSE)
  Docs: function(x, k = 5, iter = 2, squeeze = FALSE)
  Mismatches in argument default values:
    Name: 'k' Code: 2 Docs: 5

* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
getATACABsignal 29.609  0.654  31.031
getCompartments 27.816  0.350  28.171
getABSignal      7.628  0.646   8.658
getBinMatrix     6.354  0.103   6.547
plotAB           6.160  0.096   6.257
getCorMatrix     5.910  0.093   6.006
* 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/compartmap.Rcheck/00check.log’
for details.



Installation output

compartmap.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL compartmap
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘compartmap’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘compartmap_vignette.Rmd’ using ‘UTF-8’ 
** 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 (compartmap)

Tests output


Example timings

compartmap.Rcheck/compartmap-Ex.timings

nameusersystemelapsed
fisherZ0.0030.0010.003
getABSignal7.6280.6468.658
getATACABsignal29.609 0.65431.031
getBinMatrix6.3540.1036.547
getCompartments27.816 0.35028.171
getCorMatrix5.9100.0936.006
ifisherZ0.0040.0010.004
plotAB6.1600.0966.257