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This page was generated on 2022-01-24 13:08:03 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for nethet on machv2


To the developers/maintainers of the nethet package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/nethet.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1285/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nethet 1.26.0  (landing page)
Nicolas Staedler
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/nethet
git_branch: RELEASE_3_14
git_last_commit: b1233b3
git_last_commit_date: 2021-10-26 12:18:03 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: nethet
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:nethet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings nethet_1.26.0.tar.gz
StartedAt: 2022-01-23 15:49:52 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 15:53:53 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 241.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: nethet.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:nethet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings nethet_1.26.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/nethet.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.26.0’
* 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 ... 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 ‘/Users/biocbuild/bbs-3.14-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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
het_cv_glasso       30.472  0.039  30.543
mixglasso           20.138  0.772  20.923
ggmgsa_multisplit   18.195  0.021  18.227
diffregr_multisplit 12.225  0.118  12.356
diffnet_multisplit   5.237  0.013   5.254
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/nethet.Rcheck/00check.log’
for details.



Installation output

nethet.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL nethet
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘nethet’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c betamat_diffnet.c -o betamat_diffnet.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o nethet.so betamat_diffnet.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 18 ]
> 
> proc.time()
   user  system elapsed 
 11.291   0.493  11.767 

Example timings

nethet.Rcheck/nethet-Ex.timings

nameusersystemelapsed
aggpval0.0090.0010.010
bwprun_mixglasso3.5860.1883.776
diffnet_multisplit5.2370.0135.254
diffnet_singlesplit2.7480.0062.755
diffregr_multisplit12.225 0.11812.356
diffregr_singlesplit0.7250.0040.730
dot_plot0.9760.0130.992
export_network0.2430.0070.252
generate_2networks0.0550.0020.057
generate_inv_cov0.1060.2360.342
ggmgsa_multisplit18.195 0.02118.227
gsea.iriz0.0130.0020.015
het_cv_glasso30.472 0.03930.543
invcov2parcor0.0010.0000.002
invcov2parcor_array0.0070.0000.008
logratio0.0020.0000.002
mixglasso20.138 0.77220.923
plot_2networks0.0540.0020.055
scatter_plot2.0140.0252.095
screen_aic.glasso0.9570.0090.967
screen_bic.glasso1.0200.0031.024
screen_cv.glasso2.0280.0062.036
screen_cv1se.lasso0.2160.0020.219
screen_cvfix.lasso0.2070.0000.207
screen_cvmin.lasso0.2030.0020.206
screen_cvsqrt.lasso0.1830.0020.184
screen_cvtrunc.lasso0.1490.0010.149
sim_mix0.0040.0080.012
sim_mix_networks0.0110.0020.013