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### Running command:
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###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Pigengene.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Pigengene_1.20.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/Pigengene.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Pigengene/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Pigengene' version '1.20.0'
* 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 'Pigengene' can be installed ... OK
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
'library' or 'require' calls in package code:
  'AnnotationDbi' 'biomaRt' 'energy' 'org.Hs.eg.db' 'org.Mm.eg.db'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'BiocStyle'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Found the following possibly unsafe calls:
File 'Pigengene/R/bn.calculation.R':
  assignInNamespace("supported.clusters", fixArgs, "bnlearn")

apply.filter: no visible binding for global variable 'epsilon'
get.enriched.pw: no visible global function definition for 'enrichNCG'
one.step.pigengene: no visible binding for global variable
  'org.Hs.eg.db'
Undefined global functions or variables:
  enrichNCG epsilon org.Hs.eg.db
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
Pigengene-package  68.44   3.49   72.97
one.step.pigengene 64.17   2.60   67.71
module.heatmap     40.28   4.54   45.04
gene.mapping       29.43   1.14   36.09
learn.bn           16.28   0.06   17.06
compact.tree       14.50   0.08   14.58
make.decision.tree 13.00   0.27   13.27
combine.networks   11.53   0.00   11.63
wgcna.one.step     10.00   0.03   10.04
pigengene           6.95   0.48    7.44
compute.pigengene   6.31   0.41    6.72
plot.pigengene      6.01   0.36    6.38
project.eigen       5.75   0.29    6.04
get.enriched.pw     1.53   0.18    6.86
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
one.step.pigengene 69.70   2.55   91.35
Pigengene-package  68.65   1.88   71.73
module.heatmap     39.72   4.67   53.03
gene.mapping       19.40   0.56   22.82
learn.bn           17.28   0.06   18.53
make.decision.tree 14.55   0.11   14.67
compact.tree       13.17   0.19   13.36
combine.networks   12.66   0.02   12.71
wgcna.one.step     10.33   0.00   10.33
compute.pigengene   6.56   0.40    7.05
pigengene           6.21   0.36    6.84
plot.pigengene      5.36   0.32    5.67
project.eigen       4.89   0.17    5.09
get.enriched.pw     1.63   0.20    6.79
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/Pigengene.Rcheck/00check.log'
for details.