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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_1.36.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/nethet.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘nethet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘nethet’ version ‘1.36.0’
* 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 ‘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 ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/nethet.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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) 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_ncomp_fixed.Rd:22: Lost braces; missing escapes or markup?
    22 | init={'cl.init','r.means','random','kmeans','kmeans.hc','hc'}. Default='kmeans'}
       |      ^
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) NetHet-package.Rd:19: Lost braces
    19 | St{\"a}dler, N. and Mukherjee, S. (2013). Two-Sample Testing in High-Dimensional Models.
       |   ^
* 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 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     13.020  0.006  13.026
ggmgsa_multisplit  8.378  0.009   8.389
mixglasso          4.761  0.244   5.007
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/nethet.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL nethet
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘nethet’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c betamat_diffnet.c -o betamat_diffnet.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/4.4-arm64/Resources/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)

R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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.

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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 
  3.498   0.187   3.688