##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:IHWpaper.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings IHWpaper_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-data-experiment/meat/IHWpaper.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘IHWpaper/DESCRIPTION’ ... OK
* this is package ‘IHWpaper’ version ‘1.26.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘IHWpaper’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 72.8Mb
  sub-directories of 1Mb or more:
    extdata  70.6Mb
    libs      1.2Mb
* 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 loading without being on the library search path ... 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
scott_fdrreg: no visible global function definition for ‘FDRreg’
scott_fdrreg: no visible global function definition for ‘getFDR’
sim_fun_eval: no visible binding for global variable ‘fdr_method’
sim_fun_eval: no visible binding for global variable ‘fdr_pars’
sim_fun_eval: no visible binding for global variable ‘FDP’
sim_fun_eval: no visible binding for global variable ‘power’
sim_fun_eval: no visible binding for global variable ‘rj_ratio’
sim_fun_eval: no visible binding for global variable ‘FPR’
sim_fun_eval: no visible global function definition for ‘sd’
sim_fun_eval: no visible binding for global variable ‘FWER’
Undefined global functions or variables:
  FDP FDRreg FPR FWER fdr_method fdr_pars getFDR power rj_ratio sd
Consider adding
  importFrom("stats", "power", "sd")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
analyze_dataset 10.791    0.4  11.192
* 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 ...
  ‘BH-explanation.Rmd’... OK
  ‘IHW_bonferroni_simulations.Rmd’... OK
  ‘explaining_tdr.Rmd’... OK
  ‘grenander_vs_ecdf.Rmd’... OK
  ‘hqtl_IHW_BY.Rmd’ using ‘UTF-8’... OK
  ‘real_data_examples.Rmd’... OK
  ‘real_data_examples_single_curve.Rmd’... OK
  ‘simulations_vignette.Rmd’... OK
  ‘stratified_histograms.Rmd’... OK
  ‘tdr_pvalue_rejection_thresholds.Rmd’... OK
  ‘weights_vs_filtering.Rmd’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-data-experiment/meat/IHWpaper.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL IHWpaper
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘IHWpaper’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ddhf.cpp -o ddhf.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o IHWpaper.so RcppExports.o ddhf.o -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/site-library/00LOCK-IHWpaper/00new/IHWpaper/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (IHWpaper)

R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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("IHWpaper")
Loading required package: IHW
> 
> test_check("IHWpaper")
[1] "BH"
[1] "LSL GBH"
[1] "TST GBH"
[1] "SBH"
[1] "Clfdr"
[1] "Greedy Indep. Filt."
[1] "IHW"
[1] "IHW-Bonferroni E3"
[1] "Bonferroni"
[1] "qvalue"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
 49.140   1.108  50.281