Package: phenopath

Version: 1.6.7

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:phenopath.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings phenopath_1.6.7.tar.gz

StartedAt: 2019-04-16 02:04:29 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 02:06:43 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 134.4 seconds

RetCode: 0

Status:  OK

CheckDir: phenopath.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:phenopath.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings phenopath_1.6.7.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/phenopath.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phenopath/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘phenopath’ version ‘1.6.7’
* 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 ‘phenopath’ can be installed ... OK
* 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 ... 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
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/phenopath.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL phenopath
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘phenopath’ ...
** libs
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c cavi.cpp -o cavi.o
g++ -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o phenopath.so RcppExports.o cavi.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/phenopath/libs
** R
** 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 (phenopath)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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(phenopath)
> 
> test_check("phenopath")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 26 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  6.388   0.272   6.663 

name	user	system	elapsed
clvm	1.856	0.020	1.889
interaction_effects	0.084	0.000	0.083
interaction_sds	0.084	0.000	0.085
interactions	0.216	0.016	0.232
phenopath	0.096	0.008	0.103
plot_elbo	1.316	0.000	1.318
print.phenopath_fit	0.088	0.000	0.086
significant_interactions	0.092	0.000	0.093
simulate_phenopath	0.004	0.000	0.004
trajectory	0.156	0.000	0.154