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### Running command:
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###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GmicR.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GmicR_1.19.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/GmicR.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 'GmicR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GmicR' version '1.19.0'
* package encoding: UTF-8
* 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 'GmicR' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'ape::degree' by 'bnlearn::degree' when loading 'GmicR'
See 'C:/Users/biocbuild/bbs-3.20-bioc/meat/GmicR.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  GPL-2 + file LICENSE
* 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 ... NOTE
Namespace in Imports field not imported from: 'data.table'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GSEAGO_Builder: no visible binding for global variable 'ex'
Undefined global functions or variables:
  ex
* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
GSEAGO_Builder 44.71  44.89  583.91
Auto_WGCNA     13.51   0.11   14.76
InverseARCs     7.86   0.12    8.03
bn_tabu_gen     2.44   1.40  202.20
* 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, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/GmicR.Rcheck/00check.log'
for details.

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### Running command:
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###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL GmicR
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* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'GmicR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'ape::degree' by 'bnlearn::degree' when loading 'GmicR'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'ape::degree' by 'bnlearn::degree' when loading 'GmicR'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'ape::degree' by 'bnlearn::degree' when loading 'GmicR'
** testing if installed package keeps a record of temporary installation path
* DONE (GmicR)