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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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

Package 1407/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nethet 1.38.0  (landing page)
Nicolas Staedler
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/nethet
git_branch: RELEASE_3_20
git_last_commit: df04fd9
git_last_commit_date: 2024-10-29 09:57:17 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for nethet on nebbiolo2

To the developers/maintainers of the nethet package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: nethet
Version: 1.38.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:nethet.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings nethet_1.38.0.tar.gz
StartedAt: 2024-12-20 03:34:36 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 03:43:55 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 558.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: nethet.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:nethet.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings nethet_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/nethet.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘nethet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘nethet’ version ‘1.38.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘limma::logsumexp’ by ‘mclust::logsumexp’ when loading ‘nethet’
  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-3.20-bioc/meat/nethet.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 code 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
screen_shrink: no visible global function definition for
  ‘performance.pcor’
Undefined global functions or variables:
  performance.pcor
* checking Rd files ... NOTE
checkRd: (-1) NetHet-package.Rd:19: Lost braces
    19 | St{\"a}dler, N. and Mukherjee, S. (2013). Two-Sample Testing in High-Dimensional Models.
       |   ^
checkRd: (-1) bwprun_mixglasso.Rd:32: Lost braces; missing escapes or markup?
    32 | init={'cl.init','r.means','random','kmeans','kmeans.hc','hc'}. Default='kmeans.hc'}
       |      ^
checkRd: (-1) func.uinit.Rd:16: Lost braces; missing escapes or markup?
    16 | init={'cl.init','r.means','random','kmeans','kmeans.hc','hc'}}
       |      ^
checkRd: (-1) mixglasso.Rd:31: Lost braces; missing escapes or markup?
    31 | init={'cl.init','r.means','random','kmeans','kmeans.hc','hc'}. Default='kmeans'}
       |      ^
checkRd: (-1) mixglasso_ncomp_fixed.Rd:22: Lost braces; missing escapes or markup?
    22 | init={'cl.init','r.means','random','kmeans','kmeans.hc','hc'}. Default='kmeans'}
       |      ^
* checking Rd metadata ... NOTE
Invalid package aliases in Rd file 'NetHet-package.Rd':
  ‘NetHet-package’
* 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       27.644  0.181  27.828
ggmgsa_multisplit   17.126  0.014  17.142
mixglasso           13.858  0.095  13.953
diffregr_multisplit  5.689  0.116   5.806
diffnet_multisplit   5.099  0.063   5.163
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/nethet.Rcheck/00check.log’
for details.


Installation output

nethet.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL nethet
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘nethet’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/biocbuild/bbs-3.20-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-3.20-bioc/R/lib -L/usr/local/lib -o nethet.so betamat_diffnet.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-nethet/00new/nethet/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘limma::logsumexp’ by ‘mclust::logsumexp’ when loading ‘nethet’
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 ‘limma::logsumexp’ by ‘mclust::logsumexp’ when loading ‘nethet’
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 ‘limma::logsumexp’ by ‘mclust::logsumexp’ when loading ‘nethet’
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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 'limma::logsumexp' by 'mclust::logsumexp' when loading 'nethet' 
2: replacing previous import 'mclust::dmvnorm' by 'mvtnorm::dmvnorm' when loading 'nethet' 
3: 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 
  6.707   0.311   7.003 

Example timings

nethet.Rcheck/nethet-Ex.timings

nameusersystemelapsed
aggpval0.0050.0000.005
bwprun_mixglasso1.7840.0431.827
diffnet_multisplit5.0990.0635.163
diffnet_singlesplit2.6470.0482.695
diffregr_multisplit5.6890.1165.806
diffregr_singlesplit0.4190.0030.422
dot_plot0.6840.0090.693
export_network0.150.000.15
generate_2networks0.0310.0010.031
generate_inv_cov0.0330.0180.051
ggmgsa_multisplit17.126 0.01417.142
gsea.iriz0.0040.0010.005
het_cv_glasso27.644 0.18127.828
invcov2parcor0.0010.0000.001
invcov2parcor_array0.0050.0000.004
logratio0.0010.0000.000
mixglasso13.858 0.09513.953
plot_2networks0.030.000.03
scatter_plot1.1230.0161.139
screen_aic.glasso0.8870.0000.888
screen_bic.glasso0.8660.0000.866
screen_cv.glasso1.8660.0001.866
screen_cv1se.lasso0.1020.0000.102
screen_cvfix.lasso0.0990.0000.099
screen_cvmin.lasso0.1090.0000.109
screen_cvsqrt.lasso0.1010.0000.102
screen_cvtrunc.lasso0.1090.0000.110
sim_mix0.0010.0010.002
sim_mix_networks0.0070.0000.007