Package: IHWpaper

Version: 1.7.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:IHWpaper.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings IHWpaper_1.7.0.tar.gz

StartedAt: 2018-04-19 11:03:41 -0400 (Thu, 19 Apr 2018)

EndedAt: 2018-04-19 11:07:17 -0400 (Thu, 19 Apr 2018)

EllapsedTime: 215.3 seconds

RetCode: 0

Status:  OK

CheckDir: IHWpaper.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:IHWpaper.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings IHWpaper_1.7.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-data-experiment/meat/IHWpaper.Rcheck’
* using R version 3.5.0 beta (2018-04-09 r74567)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IHWpaper/DESCRIPTION’ ... OK
* this is package ‘IHWpaper’ version ‘1.7.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘IHWpaper’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.5Mb
  sub-directories of 1Mb or more:
    extdata   9.8Mb
* 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
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 ‘rj_ratio’
sim_fun_eval: no visible binding for global variable ‘FPR’
sim_fun_eval: no visible binding for global variable ‘FWER’
Undefined global functions or variables:
  FDP FDRreg FPR FWER fdr_method fdr_pars getFDR rj_ratio
* 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 or elapsed time > 5s
                user system elapsed
analyze_dataset 6.74  0.044   6.871
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-data-experiment/meat/IHWpaper.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL IHWpaper
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘IHWpaper’ ...
** libs
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -c ddhf.cpp -o ddhf.o
g++ -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o IHWpaper.so RcppExports.o ddhf.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/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
* DONE (IHWpaper)

R version 3.5.0 beta (2018-04-09 r74567) -- "Joy in Playing"
Copyright (C) 2018 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"
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 1 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
291.468   1.260  91.985 

name	user	system	elapsed
analyze_dataset	6.740	0.044	6.871
bh	0.036	0.004	0.041
bonf	0.040	0.008	0.047
clfdr	0.108	0.000	0.107
continuous_wrap	0.096	0.000	0.092
ddhf	1.612	0.000	1.613
du_ttest_sim	0.032	0.000	0.032
gbh	0.06	0.00	0.06
ihw_naive	2.828	0.104	0.664
lsl_pi0_est	0.040	0.000	0.038
null_sim	0.004	0.000	0.002
pretty_legend	0.62	0.00	1.24
run_evals	1.128	0.000	1.131
storey_qvalue	0.056	0.000	0.057
stratified_bh	0.064	0.000	0.066
tst_pi0_est	0.036	0.004	0.042
wasserman_normal_prds_sim	0.016	0.000	0.016
wasserman_normal_sim	0.004	0.000	0.006