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### Running command:
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###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MethCP.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings MethCP_1.12.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/MethCP.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MethCP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MethCP' version '1.12.0'
* 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 'MethCP' can be installed ... WARNING
Found the following significant warnings:
  Note: possible error in 'DMLtest(o, group1, group2, ': unused argument (BPPARAM = bpparam()) 
See 'F:/biocbuild/bbs-3.16-bioc/meat/MethCP.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
* checking installed package size ... NOTE
  installed size is 17.3Mb
  sub-directories of 1Mb or more:
    extdata  16.9Mb
* 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
* 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
calcLociStat : <anonymous>: possible error in DMLtest(o, group1,
  group2, equal.disp = FALSE, smoothing = FALSE, BPPARAM = bpparam()):
  unused argument (BPPARAM = bpparam())
createBsseqObject: no visible binding for global variable 'plogis'
createBsseqObject: no visible global function definition for
  'combineList'
Undefined global functions or variables:
  combineList plogis
Consider adding
  importFrom("stats", "plogis")
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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
getSigRegion           2.55   0.12   35.81
segmentMethCP          2.62   0.05   36.06
calcLociStat           2.35   0.08   20.44
calcLociStatTimeCourse 1.43   0.09   23.29
* 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:
  The following objects are masked from 'package:matrixStats':
  
      anyMissing, rowMedians
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 15 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-MethCP.R:25:5'): methylKit ───────────────────────────────────
  `methcp_obj2 <- segmentMethCP(methcp_obj2, bs_object, region.test = "fisher")` produced warnings.
  ── Failure ('test-MethCPTimeCourse.R:8:5'): methylKit ──────────────────────────
  `obj_ts <- segmentMethCP(obj_ts, bs_object_ts, region.test = "stouffer")` produced warnings.
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 15 ]
  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-3.16-bioc/meat/MethCP.Rcheck/00check.log'
for details.