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CHECK report for nethet on malbec2

This page was generated on 2020-10-17 11:55:15 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE nethet PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1187/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nethet 1.20.1
Nicolas Staedler
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/nethet
Branch: RELEASE_3_11
Last Commit: 0c592f9
Last Changed Date: 2020-09-29 16:40:59 -0400 (Tue, 29 Sep 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: nethet
Version: 1.20.1
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:nethet.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings nethet_1.20.1.tar.gz
StartedAt: 2020-10-17 03:39:20 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:42:49 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 208.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: nethet.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:nethet.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings nethet_1.20.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/nethet.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘nethet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘nethet’ version ‘1.20.1’
* 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 ‘nethet’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘mclust::dmvnorm’ by ‘mvtnorm::dmvnorm’ when loading ‘nethet’
  Warning: replacing previous import ‘multtest::update’ by ‘stats::update’ when loading ‘nethet’
See ‘/home/biocbuild/bbs-3.11-bioc/meat/nethet.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 ... NOTE
screen_shrink: no visible global function definition for
  ‘performance.pcor’
Undefined global functions or variables:
  performance.pcor
* 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
het_cv_glasso       32.188  0.003  32.210
ggmgsa_multisplit   19.982  0.001  19.985
mixglasso           12.827  0.112  12.939
diffregr_multisplit  9.145  0.032   9.177
diffnet_multisplit   5.202  0.000   5.202
* 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 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/nethet.Rcheck/00check.log’
for details.



Installation output

nethet.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL nethet
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘nethet’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c betamat_diffnet.c -o betamat_diffnet.o
gcc -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o nethet.so betamat_diffnet.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-nethet/00new/nethet/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘mclust::dmvnorm’ by ‘mvtnorm::dmvnorm’ when loading ‘nethet’
Warning: replacing previous import ‘multtest::update’ by ‘stats::update’ when loading ‘nethet’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘mclust::dmvnorm’ by ‘mvtnorm::dmvnorm’ when loading ‘nethet’
Warning: replacing previous import ‘multtest::update’ by ‘stats::update’ when loading ‘nethet’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘mclust::dmvnorm’ by ‘mvtnorm::dmvnorm’ when loading ‘nethet’
Warning: replacing previous import ‘multtest::update’ by ‘stats::update’ when loading ‘nethet’
** testing if installed package keeps a record of temporary installation path
* DONE (nethet)

Tests output

nethet.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(nethet)
Warning messages:
1: replacing previous import 'mclust::dmvnorm' by 'mvtnorm::dmvnorm' when loading 'nethet' 
2: replacing previous import 'multtest::update' by 'stats::update' when loading 'nethet' 
> 
> test_check("nethet")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 18 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  9.158   0.254   9.411 

Example timings

nethet.Rcheck/nethet-Ex.timings

nameusersystemelapsed
aggpval0.0050.0000.005
bwprun_mixglasso2.9130.0282.955
diffnet_multisplit5.2020.0005.202
diffnet_singlesplit2.4340.0002.435
diffregr_multisplit9.1450.0329.177
diffregr_singlesplit0.6440.0000.644
dot_plot0.6090.0030.613
export_network0.1580.0010.158
generate_2networks0.0370.0000.038
generate_inv_cov0.0720.0230.096
ggmgsa_multisplit19.982 0.00119.985
gsea.iriz0.0070.0000.006
het_cv_glasso32.188 0.00332.210
invcov2parcor0.0010.0000.001
invcov2parcor_array0.0050.0000.005
logratio0.0010.0000.001
mixglasso12.827 0.11212.939
plot_2networks0.0590.0000.060
scatter_plot1.5150.0041.518
screen_aic.glasso1.1520.0001.152
screen_bic.glasso1.0590.0001.059
screen_cv.glasso2.2590.0002.260
screen_cv1se.lasso0.2250.0000.224
screen_cvfix.lasso0.2240.0000.224
screen_cvmin.lasso0.230.000.23
screen_cvsqrt.lasso0.220.000.22
screen_cvtrunc.lasso0.2150.0000.215
sim_mix0.0060.0000.006
sim_mix_networks0.0190.0000.020