Package: DBChIP

Version: 1.31.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DBChIP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DBChIP_1.31.0.tar.gz

StartedAt: 2020-01-16 03:29:59 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 03:33:48 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 228.7 seconds

RetCode: 0

Status:  OK

CheckDir: DBChIP.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DBChIP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DBChIP_1.31.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/DBChIP.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 ‘DBChIP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DBChIP’ version ‘1.31.0’
* 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 ‘DBChIP’ 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
'library' or 'require' calls to packages already attached by Depends:
  ‘DESeq’ ‘edgeR’
  Please remove these calls from your code.
'library' or 'require' call to ‘ShortRead’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bin.data: no visible global function definition for ‘hist’
comp.bkg.size : <anonymous>: no visible global function definition for
  ‘hist’
est.common.disp.by.collapse: no visible global function definition for
  ‘combn’
est.common.disp.by.collapse: no visible global function definition for
  ‘model.matrix’
est.common.disp.by.collapse: no visible global function definition for
  ‘quantile’
get.chr.site.count: no visible global function definition for ‘hist’
get.chr.unique.read.count: no visible global function definition for
  ‘hist’
get.cluster: no visible global function definition for ‘dist’
get.cluster: no visible global function definition for ‘hclust’
get.cluster: no visible global function definition for ‘cutree’
get.cluster: no visible global function definition for ‘weighted.mean’
get.coverage: no visible global function definition for ‘hist’
get.coverage: no visible global function definition for ‘convolve’
median.ratio : <anonymous>: no visible global function definition for
  ‘median’
read.AlignedRead: no visible global function definition for ‘is’
read.AlignedRead: no visible global function definition for ‘position’
read.AlignedRead: no visible global function definition for ‘strand’
read.AlignedRead: no visible global function definition for ‘width’
read.AlignedRead: no visible global function definition for
  ‘chromosome’
read.BED: no visible global function definition for ‘read.delim’
single.peak: no visible global function definition for ‘par’
single.peak: no visible global function definition for ‘matplot’
single.peak: no visible global function definition for ‘abline’
single.peak: no visible global function definition for ‘mtext’
site.merge : <anonymous>: no visible global function definition for
  ‘weighted.mean’
test.diff.binding.2sample : <anonymous>: no visible global function
  definition for ‘binom.test’
test.diff.binding.DESeq: no visible global function definition for
  ‘pData’
test.diff.binding.DESeq: no visible global function definition for
  ‘pData<-’
test.diff.binding.edgeR: no visible global function definition for
  ‘model.matrix’
Undefined global functions or variables:
  abline binom.test chromosome combn convolve cutree dist hclust hist
  is matplot median model.matrix mtext pData pData<- par position
  quantile read.delim strand weighted.mean width
Consider adding
  importFrom("graphics", "abline", "hist", "matplot", "mtext", "par")
  importFrom("methods", "is")
  importFrom("stats", "binom.test", "convolve", "cutree", "dist",
             "hclust", "median", "model.matrix", "quantile",
             "weighted.mean")
  importFrom("utils", "combn", "read.delim")
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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/DBChIP.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 DBChIP
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘DBChIP’ ...
** using staged installation
** 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 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 (DBChIP)

R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("DBChIP") || stop("unable to load DBChIP")
Loading required package: DBChIP
Loading required package: edgeR
Loading required package: limma
Loading required package: DESeq
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:limma':

    plotMA

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: lattice
    Welcome to 'DESeq'. For improved performance, usability and
    functionality, please consider migrating to 'DESeq2'.
[1] TRUE
> BiocGenerics:::testPackage("DBChIP")
merging sites from different conditions to consensus sites.done
reading data...done
computing normalization factor between ChIP and control samples.done
count ChIP reads around each binding site.done


RUNIT TEST PROTOCOL -- Thu Jan 16 03:33:39 2020 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
DBChIP RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  8.505   0.856   9.308 

name	user	system	elapsed
DBChIP-package	1.016	0.100	1.118
DBChIP	3.677	0.628	4.328
binding.site.list	0.308	0.040	0.349
chip.data.list	0.299	0.033	0.331
conds	0.310	0.034	0.347
input.data.list	0.303	0.028	0.331
load.data	0.542	0.101	0.644
read.binding.site.list	0.338	0.046	0.383