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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_1.33.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/Pigengene.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* 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 ‘1.33.0’
* 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:25-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:27-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:30-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:42-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:45-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:50-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:53-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:56-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:58-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:60-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:64-68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:73-76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:77-79: 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
Pigengene-package  76.819  2.877  80.355
get.enriched.pw    72.241  6.310  79.434
one.step.pigengene 74.613  2.458  77.547
module.heatmap     34.409  1.804  36.510
learn.bn           15.608  0.380  16.111
make.filter        15.081  0.327  15.505
apply.filter       14.022  0.284  14.372
combine.networks   13.537  0.106  13.730
determine.modules  12.966  0.119  13.167
wgcna.one.step     12.923  0.074  13.055
compute.pigengene  11.831  0.732  12.642
make.decision.tree 11.849  0.594  12.536
compact.tree       11.717  0.699  12.534
gene.mapping        7.806  0.848  10.538
pigengene           6.521  0.558   7.132
plot.pigengene      6.527  0.358   6.936
project.eigen       5.995  0.361   6.396
* 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-3.21-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/4.5-x86_64/Resources/library’
* installing *source* package ‘Pigengene’ ...
** this is package ‘Pigengene’ version ‘1.33.0’
** 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)