Package: ChIC

Version: 1.3.33

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ChIC.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ChIC_1.3.33.tar.gz

StartedAt: 2019-04-08 23:20:39 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 23:22:48 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 129.2 seconds

RetCode: 0

Status:  OK

CheckDir: ChIC.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ChIC.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ChIC_1.3.33.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ChIC.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIC/DESCRIPTION’ ... OK
* this is package ‘ChIC’ version ‘1.3.33’
* 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 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/ChIC.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL ChIC
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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
createMetageneProfile	0.001	0.000	0.001
getCrossCorrelationScores	0.001	0.000	0.001
getPeakCallingScores	0	0	0
listAvailableElements	0.013	0.000	0.013
listDatasets	0.141	0.024	0.187
metagenePlotsForComparison	0.001	0.000	0.001
plotReferenceDistribution	0	0	0
predictionScore	0	0	0
qualityScores_EM	0.000	0.000	0.001
qualityScores_GM	0.001	0.000	0.000
qualityScores_LM	0	0	0
qualityScores_LMgenebody	0.001	0.000	0.001
readBamFile	0	0	0
removeLocalTagAnomalies	0	0	0
tagDensity	0.001	0.000	0.001