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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Pigengene_1.30.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/Pigengene.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Pigengene/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Pigengene’ version ‘1.30.0’
* 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 ‘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 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
'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.
* 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")

one.step.pigengene: no visible binding for global variable
  ‘org.Hs.eg.db’
Undefined global functions or variables:
  org.Hs.eg.db
* checking Rd files ... NOTE
checkRd: (-1) draw.bn.Rd:47: Lost braces
    47 |      rename the nodes name.  See code{rename.node}.}
       |                                      ^
checkRd: (-1) eigengenes33.Rd:21-22: Lost braces
    21 |  {A 202 by 34 matrix. 
       |  ^
checkRd: (-1) eigengenes33.Rd:25: Lost braces; missing escapes or markup?
    25 |  {A 164 by 34 matrix for MDS cases with columns similar to aml.}
       |  ^
checkRd: (-1) eigengenes33.Rd:28: Lost braces; missing escapes or markup?
    28 |  {A numeric vector of length 9166 labeling members of each module. Named by Entrez ID.}
       |  ^
checkRd: (-1) pigengene-class.Rd:22-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:24-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:27-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:35-36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:37-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:40-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:45-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:48-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:51-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:55-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:59-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:68-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:72-74: Lost braces in \itemize; meant \describe ?
* 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 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
get.enriched.pw    135.541 11.118 177.307
Pigengene-package  100.166  3.480 129.876
one.step.pigengene 100.257  2.699 115.095
module.heatmap      76.724  2.338  87.472
make.decision.tree  20.964  0.579  23.493
compact.tree        20.847  0.597  26.252
learn.bn            18.315  0.465  21.431
make.filter         17.977  0.387  20.387
apply.filter        16.451  0.362  20.357
combine.networks    15.107  0.166  18.556
gene.mapping        13.661  1.444  80.160
determine.modules   14.036  0.133  17.346
wgcna.one.step      13.181  0.104  14.629
pigengene           10.373  0.782  12.797
plot.pigengene      10.610  0.418  12.054
compute.pigengene   10.223  0.469  13.003
project.eigen        9.470  0.396  10.753
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/Pigengene.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Pigengene
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘Pigengene’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Pigengene)