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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:nethet.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings nethet_1.38.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/nethet.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'nethet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'nethet' version '1.38.0'
* 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 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 'F:/biocbuild/bbs-3.20-bioc/meat/nethet.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* 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 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 for x64 is not available
File 'F:/biocbuild/bbs-3.20-bioc/R/library/nethet/libs/x64/nethet.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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       35.48   0.00   35.52
ggmgsa_multisplit   20.98   0.00   20.99
mixglasso           17.47   0.71   18.19
diffregr_multisplit  6.81   0.25    7.06
diffnet_multisplit   6.26   0.02    6.28
* 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
  'F:/biocbuild/bbs-3.20-bioc/meat/nethet.Rcheck/00check.log'
for details.