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CHECK report for ChIC on merida1

This page was generated on 2020-08-12 12:02:46 -0400 (Wed, 12 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ChIC PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 266/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIC 1.9.0
Carmen Maria Livi
Snapshot Date: 2020-08-11 14:50:16 -0400 (Tue, 11 Aug 2020)
URL: https://git.bioconductor.org/packages/ChIC
Branch: master
Last Commit: 6e3b94c
Last Changed Date: 2020-04-27 15:15:51 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64 ...NOT SUPPORTED...
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ChIC
Version: 1.9.0
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_1.9.0.tar.gz
StartedAt: 2020-08-12 03:53:36 -0400 (Wed, 12 Aug 2020)
EndedAt: 2020-08-12 03:56:30 -0400 (Wed, 12 Aug 2020)
EllapsedTime: 173.8 seconds
RetCode: 0
Status:  OK 
CheckDir: ChIC.Rcheck
Warnings: 0

Command output

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### Running 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_1.9.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/ChIC.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIC/DESCRIPTION’ ... OK
* this is package ‘ChIC’ version ‘1.9.0’
* 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
  ‘hg38_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
  ‘mm10_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
  ‘hg38_chrom_info’
f_chromInfoLoad: no visible binding for global variable
  ‘mm9_chrom_info’
f_chromInfoLoad: no visible binding for global variable
  ‘mm10_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 hg38_chrom_info
  hg38_refseq_genes_filtered_granges mm10_chrom_info
  mm10_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-3.12-bioc/meat/ChIC.Rcheck/00check.log’
for details.



Installation output

ChIC.Rcheck/00install.out

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### Running command:
###
###   /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)

Tests output


Example timings

ChIC.Rcheck/ChIC-Ex.timings

nameusersystemelapsed
chicWrapper0.0010.0010.001
createMetageneProfile0.0000.0010.001
getCrossCorrelationScores0.0000.0010.001
getPeakCallingScores0.0010.0010.001
listAvailableElements0.0120.0050.017
listDatasets0.2210.0680.290
metagenePlotsForComparison0.0000.0010.002
plotReferenceDistribution000
predictionScore0.0010.0010.002
qualityScores_EM0.0000.0010.001
qualityScores_GM0.0010.0010.002
qualityScores_LM0.0000.0000.001
qualityScores_LMgenebody0.0000.0000.001
readBamFile0.0000.0000.001
removeLocalTagAnomalies0.0000.0010.001
tagDensity0.0000.0010.001