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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ccrepe.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ccrepe_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/ccrepe.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 'ccrepe/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ccrepe' version '1.24.0'
* 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 'ccrepe' 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
calculate.z.stat.and.p.value: no visible global function definition for
  'var'
calculate.z.stat.and.p.value: no visible global function definition for
  'pnorm'
ccrepe: no visible binding for global variable 'cor'
nc.score: no visible global function definition for 'na.omit'
nc.score: no visible global function definition for 'complete.cases'
qc_filter: no visible binding for global variable 'x'
Undefined global functions or variables:
  complete.cases cor na.omit pnorm var x
Consider adding
  importFrom("stats", "complete.cases", "cor", "na.omit", "pnorm", "var")
to your NAMESPACE file.
* 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
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
  1 Test Suite : 
  ccrepe RUnit Tests - 1 test function, 0 errors, 1 failure
  FAILURE in test.nc.score: Error in checkEquals(0, sum(abs(tau3.5 - tau3.5.check.2) > tol)) : 
    Mean absolute difference: 1
  
  
  Test files with failing tests
  
     test_nc_score.R 
       test.nc.score 
  
  
  Error in BiocGenerics:::testPackage("ccrepe") : 
    unit tests failed for package ccrepe
  Execution halted
** running tests for arch 'x64' ...
  Running 'runTests.R'
 OK
* 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 ERROR, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/ccrepe.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/ccrepe_1.24.0.tar.gz && rm -rf ccrepe.buildbin-libdir && mkdir ccrepe.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ccrepe.buildbin-libdir ccrepe_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL ccrepe_1.24.0.zip && rm ccrepe_1.24.0.tar.gz ccrepe_1.24.0.zip
###
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install for i386

* installing *source* package 'ccrepe' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ccrepe'
    finding HTML links ... done
    ccrepe-package                          html  
    ccrepe                                  html  
    ccrepeSampleTestFunction                html  
    nc.score                                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 'ccrepe' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ccrepe' as ccrepe_1.24.0.zip
* DONE (ccrepe)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'ccrepe' successfully unpacked and MD5 sums checked