Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-03-24 11:05:18 -0400 (Fri, 24 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" 4546
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" 4307
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences" 4299
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for HiTC on nebbiolo1


To the developers/maintainers of the HiTC package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HiTC.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 928/2195HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiTC 1.43.0  (landing page)
Nicolas Servant
Snapshot Date: 2023-03-23 14:00:15 -0400 (Thu, 23 Mar 2023)
git_url: https://git.bioconductor.org/packages/HiTC
git_branch: devel
git_last_commit: 5ca262b
git_last_commit_date: 2022-11-01 11:06:53 -0400 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: HiTC
Version: 1.43.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:HiTC.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings HiTC_1.43.0.tar.gz
StartedAt: 2023-03-23 21:08:18 -0400 (Thu, 23 Mar 2023)
EndedAt: 2023-03-23 21:15:48 -0400 (Thu, 23 Mar 2023)
EllapsedTime: 449.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: HiTC.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:HiTC.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings HiTC_1.43.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/HiTC.Rcheck’
* using R Under development (unstable) (2023-03-16 r83996)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘HiTC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiTC’ version ‘1.43.0’
* 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    SIGNIFICANT USER-VISIBLE CHANGES
  Cannot process chunk/lines:
    BUG FIXES
  Cannot process chunk/lines:
    NEW FEATURES
* 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 loading without being on the library search path ... 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 ... WARNING
checkRd: (5) HTClist-class.Rd:52-54: \item in \describe must have non-empty label
* 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 19.031  1.500  20.535
CQC                  5.502  0.153   5.657
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘HiC_analysis.Rnw’... OK
  ‘HiTC.Rnw’... OK
 OK
* checking re-building of vignette outputs ... NOTE
Warnings in re-building vignettes:
  Warning: file stem ‘./HiTC-plot1’ is not portable
  Warning: file stem ‘./HiTC-plot2’ is not portable
  Warning: file stem ‘./HiTC-normICE’ is not portable
  Warning: file stem ‘./HiTC-tads’ is not portable
  Warning: file stem ‘./HiTC-di’ is not portable
  Warning: file stem ‘./HiTC-qcc’ is not portable
  Warning: file stem ‘./HiTC-bin5C’ is not portable
  Warning: file stem ‘./HiTC-norm5Cznorm’ is not portable
  Warning: file stem ‘./HiTC-annot5C’ is not portable
  Warning: file stem ‘./HiTC-comp5C’ is not portable
  Warning: file stem ‘./HiTC-mapClist’ is not portable
  Warning: file stem ‘./HiTC-mapChic’ is not portable
  Warning: file stem ‘./HiTC-mapNormhic’ is not portable
  Warning: file stem ‘./HiTC-mapCorhic’ is not portable
  Warning: file stem ‘./HiTC-mapPCAhic’ is not portable
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/HiTC.Rcheck/00check.log’
for details.



Installation output

HiTC.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL HiTC
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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
CQC5.5020.1535.657
HTCexp-class2.7210.3513.074
HTClist-class1.4000.0281.435
Nora_5C0.2930.0000.293
binningC1.1820.2001.383
directionalityIndex19.031 1.50020.535
discretize000
export.my5C000
exportC0.0000.0000.001
extractRegion0.2980.0080.307
getAnnotatedRestrictionSites0.0000.0000.001
getExpectedCounts1.1180.2971.318
getPearsonMap0.5900.0720.662
getRestrictionFragmentsPerChromosome0.0000.0010.001
import.my5C0.0950.0100.105
importC0.0010.0000.000
intervalsDist1.4690.9092.377
mapC3.6690.7044.373
normICE0.0000.0010.000
normLGF0.0000.0010.000
pca.hic0.5260.0210.546
removeIntervals0.2980.0000.298
setGenomicFeatures0.0000.0000.001
setIntervalScale0.8970.0000.897