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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:normr.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings normr_1.21.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/normr.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'normr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'normr' version '1.21.0'
* 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 'normr' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'normr'
See 'D:/biocbuild/bbs-3.15-bioc/meat/normr.Rcheck/00install.out' for details.
* 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
* 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 ... WARNING
Missing link or links in documentation object 'normR-diffR.Rd':
  '[GenomeInfoDb]{fetchExtendedChromInfoFromUCSC}'

Missing link or links in documentation object 'normR-enrichR.Rd':
  '[GenomeInfoDb]{fetchExtendedChromInfoFromUCSC}'

Missing link or links in documentation object 'normR-regimeR.Rd':
  '[GenomeInfoDb]{fetchExtendedChromInfoFromUCSC}'

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.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: 2 WARNINGs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/normr.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL normr
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'normr' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -fopenmp -D_GLIBCXX_USE_C99 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -fopenmp -D_GLIBCXX_USE_C99 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c em.cpp -o em.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -fopenmp -D_GLIBCXX_USE_C99 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c normr_init.c -o normr_init.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o normr.dll tmp.def RcppExports.o em.o normr_init.o -fopenmp -D_GLIBCXX_USE_C99 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-normr/00new/normr/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'normr'
Creating a new generic function for 'getClasses' in package 'normr'
** help
*** installing help indices
  converting help for package 'normr'
    finding HTML links ... done
    NormRCountConfig-class                  html  
    NormRFit-class                          html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-normr/00new/normr/help/normRFit.html
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-normr/00new/normr/help/normrfit.html
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-normr/00new/normr/help/NormRfit.html
    normR-diffR                             html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-normr/00new/normr/help/diffr.html
    finding level-2 HTML links ... done

    normR-enrichR                           html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-normr/00new/normr/help/enrichr.html
    normR-regimeR                           html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-normr/00new/normr/help/regimer.html
    normR                                   html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-normr/00new/normr/help/normr.html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'normr'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'normr'
** testing if installed package keeps a record of temporary installation path
* DONE (normr)
Making 'packages.html' ... done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(normr)

Attaching package: 'normr'

The following object is masked from 'package:methods':

    getClasses

Warning message:
replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'normr' 
> 
> test_check("normr")
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 439 ]

== Skipped tests ===============================================================
* empty test (2)

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 439 ]
> 
> proc.time()
   user  system elapsed 
  36.23    1.14   37.59