Package: compartmap

Version: 1.0.3

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_1.0.3.tar.gz

StartedAt: 2019-04-15 23:09:27 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 23:15:59 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 391.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: compartmap.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:compartmap.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings compartmap_1.0.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/compartmap.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.0.3’
* 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 or elapsed time > 5s
                  user system elapsed
getCompartments 18.948  0.490  19.558
getATACABsignal 17.391  0.338  17.823
plotAB           5.132  0.065   5.342
getCorMatrix     5.013  0.064   5.213
* 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-3.8-bioc/meat/compartmap.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 compartmap
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘compartmap’ ...
** 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
* DONE (compartmap)

name	user	system	elapsed
fisherZ	0.002	0.000	0.002
getABSignal	4.733	0.148	4.914
getATACABsignal	17.391	0.338	17.823
getBinMatrix	4.842	0.077	4.941
getCompartments	18.948	0.490	19.558
getCorMatrix	5.013	0.064	5.213
ifisherZ	0.004	0.000	0.004
plotAB	5.132	0.065	5.342