##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:nearBynding.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings nearBynding_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/nearBynding.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'nearBynding/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'nearBynding' version '1.4.0'
* package encoding: UTF-8
* 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 'nearBynding' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.2Mb
  sub-directories of 1Mb or more:
    extdata   6.9Mb
* 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 ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
processCapRout          26.63   0.55   27.58
visualizeCapRStereogene 11.48   0.10   11.59
visualizeStereogene      9.67   0.06    9.74
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
processCapRout          23.32   0.30   23.61
visualizeCapRStereogene  9.03   0.06    9.09
visualizeStereogene      7.68   0.03    7.70
* 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-3.14-bioc/meat/nearBynding.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/nearBynding_1.4.0.tar.gz && rm -rf nearBynding.buildbin-libdir && mkdir nearBynding.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=nearBynding.buildbin-libdir nearBynding_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL nearBynding_1.4.0.zip && rm nearBynding_1.4.0.tar.gz nearBynding_1.4.0.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
  5 2944k    5  175k    0     0   515k      0  0:00:05 --:--:--  0:00:05  515k
 47 2944k   47 1405k    0     0  1041k      0  0:00:02  0:00:01  0:00:01 1040k
100 2944k  100 2944k    0     0  1408k      0  0:00:02  0:00:02 --:--:-- 1408k

install for i386

* installing *source* package 'nearBynding' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'nearBynding'
    finding HTML links ... done
    CleanBAMtoBG                            html  
    CleanBEDtoBG                            html  
    ExtractTranscriptomeSequence            html  
    GenomeMappingToChainFile                html  
    assessGrouping                          html  
    bindingContextDistance                  html  
    bindingContextDistanceCapR              html  
    getChainChrSize                         html  
    get_outfiles                            html  
    liftOverToExomicBG                      html  
    nearBynding-package                     html  
    processCapRout                          html  
    runCapR                                 html  
    runStereogene                           html  
    runStereogeneOnCapR                     html  
    symmetryCapR                            html  
    symmetryContext                         html  
    visualizeCapRStereogene                 html  
    visualizeStereogene                     html  
    write_config                            html  
    write_fasta                             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 'nearBynding' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'nearBynding' as nearBynding_1.4.0.zip
* DONE (nearBynding)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'nearBynding' successfully unpacked and MD5 sums checked