##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HiTC.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings HiTC_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/HiTC.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HiTC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HiTC' version '1.32.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
directionalityIndex 52.34   0.66   70.41
CQC                  6.00   0.22    8.78
HTClist-class        1.83   0.40    7.38
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
directionalityIndex 45.41   0.41   45.81
CQC                  7.05   0.29    8.14
* 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
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/HiTC.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/HiTC_1.32.0.tar.gz && rm -rf HiTC.buildbin-libdir && mkdir HiTC.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HiTC.buildbin-libdir HiTC_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL HiTC_1.32.0.zip && rm HiTC_1.32.0.tar.gz HiTC_1.32.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  722k  100  722k    0     0  10.6M      0 --:--:-- --:--:-- --:--:-- 11.7M

install for i386

* installing *source* package 'HiTC' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'HiTC'
    finding HTML links ... done
    CQC                                     html  
    HTCexp-class                            html  
    HTClist-class                           html  
    HiTC-internal                           html  
    Nora_5C                                 html  
    binningC                                html  
    directionalityIndex                     html  
    discretize                              html  
    export.my5C                             html  
    exportC                                 html  
    extractRegion                           html  
    getAnnotatedRestrictionSites            html  
    getExpectedCounts                       html  
    getPearsonMap                           html  
    getRestrictionFragmentsPerChromosome    html  
    import.my5C                             html  
    importC                                 html  
    intervalsDist                           html  
    mapC                                    html  
    normICE                                 html  
    normLGF                                 html  
    pca.hic                                 html  
    removeIntervals                         html  
    setGenomicFeatures                      html  
    setIntervalScale                        html  
** 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

install for x64

* installing *source* package 'HiTC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HiTC' as HiTC_1.32.0.zip
* DONE (HiTC)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'HiTC' successfully unpacked and MD5 sums checked