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CHECK report for HiTC on malbec1

This page was generated on 2021-05-06 12:27:53 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the HiTC package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 842/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiTC 1.34.0  (landing page)
Nicolas Servant
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/HiTC
Branch: RELEASE_3_12
Last Commit: b68a85e
Last Changed Date: 2020-10-27 10:45:35 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: HiTC
Version: 1.34.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:HiTC.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings HiTC_1.34.0.tar.gz
StartedAt: 2021-05-06 02:28:33 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 02:34:27 -0400 (Thu, 06 May 2021)
EllapsedTime: 353.8 seconds
RetCode: 0
Status:   OK  
CheckDir: HiTC.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:HiTC.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings HiTC_1.34.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/HiTC.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (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 ‘1.34.0’
* 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
directionalityIndex 62.52  0.436  63.127
CQC                  7.08  0.092   7.183
mapC                 5.72  0.064   5.801
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/HiTC.Rcheck/00check.log’
for details.



Installation output

HiTC.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL HiTC
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘HiTC’ ...
** using staged installation
** 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 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 (HiTC)

Tests output


Example timings

HiTC.Rcheck/HiTC-Ex.timings

nameusersystemelapsed
CQC7.0800.0927.183
HTCexp-class3.5800.1443.746
HTClist-class2.460.002.48
Nora_5C0.4080.0080.415
binningC1.8240.0001.826
directionalityIndex62.520 0.43663.127
discretize000
export.my5C000
exportC000
extractRegion0.5560.0160.572
getAnnotatedRestrictionSites000
getExpectedCounts1.6240.2921.800
getPearsonMap0.8520.0440.898
getRestrictionFragmentsPerChromosome000
import.my5C0.1680.0200.190
importC000
intervalsDist1.2920.1081.403
mapC5.7200.0645.801
normICE000
normLGF000
pca.hic0.8920.0160.909
removeIntervals0.4480.0000.447
setGenomicFeatures000
setIntervalScale1.3440.0041.348