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### Running command:
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###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:netZooR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings netZooR_1.3.1.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/netZooR.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'netZooR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'netZooR' version '1.3.1'
* 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 'netZooR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    extdata   2.8Mb
* 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 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
degreeAdjust: possible error in dim(A, 1): unused argument (1)
degreeAdjust: possible error in dim(A, 2): unused argument (2)
runEgret: no visible binding for global variable 'NA12878'
spider: no visible global function definition for 'normalizeNetwork'
spider: no visible global function definition for 'tanimoto'
spider: no visible global function definition for 'update.diagonal'
spider: no visible global function definition for 'prepResult'
Undefined global functions or variables:
  NA12878 normalizeNetwork prepResult tanimoto update.diagonal
* 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 ... WARNING
Undocumented arguments in documentation object 'pandaPy'
  'with_header'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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
monsterPlotMonsterAnalysis  38.73   0.89   39.65
monsterPrintMonsterAnalysis 35.13   0.54   35.65
pandaDiffEdges              21.89   4.53   32.75
monster                      5.63   0.29    5.92
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  ==================================================
  downloaded 7.1 MB
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 60 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-monster.R:19'): MONSTER function works ───────────────────────
  monsterTransformationMatrix(cc.net.1, cc.net.2, method = "kabsch") not equal to `monsterTM_kabsch`.
  2/2809 mismatches (average diff: 1)
  [393]  -0.00086 - 0.999 == -1
  [1121] -0.00086 - 0.999 == -1
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 60 ]
  Error: Test failures
  Execution halted
* 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 WARNING, 2 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/netZooR.Rcheck/00check.log'
for details.