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CHECK report for HiTC on merida1

This page was generated on 2019-04-16 11:56:19 -0400 (Tue, 16 Apr 2019).

Package 729/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiTC 1.26.0
Nicolas Servant
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/HiTC
Branch: RELEASE_3_8
Last Commit: be108ad
Last Changed Date: 2018-10-30 11:41:49 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: HiTC
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:HiTC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings HiTC_1.26.0.tar.gz
StartedAt: 2019-04-16 00:34:37 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:39:37 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 300.8 seconds
RetCode: 0
Status:  OK 
CheckDir: HiTC.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:HiTC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings HiTC_1.26.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/HiTC.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiTC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiTC’ version ‘1.26.0’
* 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 ... 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 ‘HiTC’ 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
directionalityIndex: no visible global function definition for
  ‘subjectHits’
directionalityIndex: no visible global function definition for
  ‘queryHits’
getBlocsIndex: no visible global function definition for ‘Rle’
getExpectedCountsMean: no visible global function definition for ‘Rle’
normLGF: no visible global function definition for ‘glm.nb’
slidingWindow: no visible binding for global variable ‘consV’
splitCombinedContacts : <anonymous>: no visible global function
  definition for ‘seqlevels<-’
divide,HTCexp-HTCexp: no visible global function definition for
  ‘queryHits’
divide,HTCexp-HTCexp: no visible global function definition for
  ‘subjectHits’
isBinned,HTCexp: no visible global function definition for
  ‘countMatches’
substract,HTCexp-HTCexp: no visible global function definition for
  ‘queryHits’
substract,HTCexp-HTCexp: no visible global function definition for
  ‘subjectHits’
Undefined global functions or variables:
  Rle consV countMatches glm.nb queryHits seqlevels<- subjectHits
* 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
Examples with CPU or elapsed time > 5s
                      user system elapsed
directionalityIndex 63.662  0.778  65.006
* 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-3.8-bioc/meat/HiTC.Rcheck/00check.log’
for details.



Installation output

HiTC.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL HiTC
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘HiTC’ ...
** 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
* DONE (HiTC)

Tests output


Example timings

HiTC.Rcheck/HiTC-Ex.timings

nameusersystemelapsed
CQC3.3860.1483.549
HTCexp-class2.6570.2132.887
HTClist-class1.4250.0611.502
Nora_5C0.3000.0030.307
binningC1.3470.0201.375
directionalityIndex63.662 0.77865.006
discretize000
export.my5C0.0000.0000.001
exportC000
extractRegion0.4110.0060.420
getAnnotatedRestrictionSites0.0000.0000.001
getExpectedCounts1.9620.5002.444
getPearsonMap0.6500.0530.712
getRestrictionFragmentsPerChromosome000
import.my5C0.1140.0140.129
importC0.0000.0010.000
intervalsDist0.4460.0450.498
mapC4.3140.4044.745
normICE000
normLGF000
pca.hic0.6270.0160.644
removeIntervals0.3400.0030.345
setGenomicFeatures0.0000.0010.000
setIntervalScale0.9320.0070.941