Back to Multiple platform build/check report for BioC 3.7
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for ChIC on malbec2

This page was generated on 2018-10-17 08:31:33 -0400 (Wed, 17 Oct 2018).

Package 223/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIC 1.0.0
Carmen Maria Livi
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/ChIC
Branch: RELEASE_3_7
Last Commit: 679f4f6
Last Changed Date: 2018-04-30 10:35:50 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 ...NOT SUPPORTED...
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ChIC
Version: 1.0.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:ChIC.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings ChIC_1.0.0.tar.gz
StartedAt: 2018-10-15 23:07:08 -0400 (Mon, 15 Oct 2018)
EndedAt: 2018-10-15 23:08:50 -0400 (Mon, 15 Oct 2018)
EllapsedTime: 101.9 seconds
RetCode: 0
Status:  OK 
CheckDir: ChIC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:ChIC.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings ChIC_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/ChIC.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.0.0’
* 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
createMetageneProfile: no visible binding for global variable
  ‘hg19_refseq_genes_filtered_granges’
f_getPredictionModel: no visible binding for global variable
  ‘rf_models’
f_loadDataCompendium: no visible binding for global variable
  ‘compendium_profiles’
plotReferenceDistribution: no visible binding for global variable
  ‘compendium_db’
tagDensity: no visible binding for global variable ‘hg19_chrom_info’
Undefined global functions or variables:
  compendium_db compendium_profiles hg19_chrom_info
  hg19_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-3.7-bioc/meat/ChIC.Rcheck/00check.log’
for details.



Installation output

ChIC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL ChIC
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘ChIC’ ...
** 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
* DONE (ChIC)

Tests output


Example timings

ChIC.Rcheck/ChIC-Ex.timings

nameusersystemelapsed
createMetageneProfile0.0000.0000.002
getCrossCorrelationScores0.0000.0000.001
getPeakCallingScores0.0000.0000.002
metagenePlotsForComparison0.0040.0000.002
plotReferenceDistribution000
predictionScore0.0040.0000.002
qualityScores_EM0.0000.0000.001
qualityScores_GM0.0000.0000.002
qualityScores_LM0.0040.0000.002
qualityScores_LMgenebody0.0000.0000.001
readBamFile0.0000.0000.001
removeLocalTagAnomalies0.0000.0000.001
tagDensity0.0000.0000.002