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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_1.29.10.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/Pigengene.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Pigengene/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Pigengene’ version ‘1.29.10’
* 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    81.121  7.321  90.019
Pigengene-package  79.756  3.269  83.702
one.step.pigengene 79.607  2.778  83.135
module.heatmap     36.305  2.158  38.884
learn.bn           15.993  0.390  16.615
make.filter        15.519  0.378  16.018
apply.filter       15.065  0.386  15.589
combine.networks   14.313  0.177  14.615
determine.modules  14.029  0.186  14.334
make.decision.tree 13.225  0.702  14.092
compact.tree       12.354  0.731  13.367
wgcna.one.step     12.866  0.124  13.082
gene.mapping        8.506  1.008  37.285
plot.pigengene      7.372  0.451   7.904
pigengene           6.898  0.664   7.660
project.eigen       7.045  0.467   7.594
compute.pigengene   6.578  0.483   7.125
* 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)