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### Running command:
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###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:HiTC.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings HiTC_1.42.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/HiTC.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘HiTC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiTC’ version ‘1.42.0’
* 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 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 ... 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 16.804  0.504  17.309
CQC                  6.534  0.100   6.635
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/HiTC.Rcheck/00check.log’
for details.