Package: ChIC

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChIC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChIC_1.7.0.tar.gz

StartedAt: 2020-01-16 02:42:05 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 02:45:43 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 218.3 seconds

RetCode: 0

Status:  OK

CheckDir: ChIC.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:ChIC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChIC_1.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/ChIC.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 ‘ChIC/DESCRIPTION’ ... OK
* this is package ‘ChIC’ version ‘1.7.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ChIC’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
f_annotationLoad: no visible binding for global variable
  ‘hg19_refseq_genes_filtered_granges’
f_annotationLoad: no visible binding for global variable
  ‘mm9_refseq_genes_filtered_granges’
f_annotationLoad: no visible binding for global variable
  ‘dm3_refseq_genes_filtered_granges’
f_chromInfoLoad: no visible binding for global variable
  ‘hg19_chrom_info’
f_chromInfoLoad: no visible binding for global variable
  ‘mm9_chrom_info’
f_chromInfoLoad: no visible binding for global variable
  ‘dm3_chrom_info’
f_getPredictionModel: no visible binding for global variable
  ‘rf_models’
f_loadDataCompendium: no visible binding for global variable
  ‘compendium_profiles’
f_loadDataCompendium: no visible binding for global variable
  ‘compendium_profiles_TF’
f_metaGeneDefinition: no visible binding for global variable
  ‘classesDefList’
plotReferenceDistribution: no visible binding for global variable
  ‘compendium_db_tf’
plotReferenceDistribution: no visible binding for global variable
  ‘compendium_db’
Undefined global functions or variables:
  classesDefList compendium_db compendium_db_tf compendium_profiles
  compendium_profiles_TF dm3_chrom_info
  dm3_refseq_genes_filtered_granges hg19_chrom_info
  hg19_refseq_genes_filtered_granges mm9_chrom_info
  mm9_refseq_genes_filtered_granges rf_models
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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/ChIC.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 ChIC
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘ChIC’ ...
** using staged installation
** R
** 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 (ChIC)

name	user	system	elapsed
chicWrapper	0.000	0.001	0.001
createMetageneProfile	0.001	0.001	0.002
getCrossCorrelationScores	0.001	0.001	0.001
getPeakCallingScores	0.001	0.001	0.002
listAvailableElements	0.016	0.006	0.025
listDatasets	0.260	0.097	0.369
metagenePlotsForComparison	0.001	0.002	0.002
plotReferenceDistribution	0.001	0.000	0.000
predictionScore	0.001	0.001	0.002
qualityScores_EM	0.001	0.001	0.001
qualityScores_GM	0.001	0.001	0.002
qualityScores_LM	0.001	0.000	0.001
qualityScores_LMgenebody	0.001	0.001	0.002
readBamFile	0.001	0.001	0.001
removeLocalTagAnomalies	0.001	0.001	0.002
tagDensity	0.001	0.001	0.002