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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings Pigengene_1.25.10.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/Pigengene.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘Pigengene/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Pigengene’ version ‘1.25.10’
* 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 R 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")

compute.pigengene: no visible global function definition for ‘prcomp’
one.step.pigengene: no visible binding for global variable
  ‘org.Hs.eg.db’
Undefined global functions or variables:
  org.Hs.eg.db prcomp
Consider adding
  importFrom("stats", "prcomp")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) get.enriched.pw.Rd:71: Escaped LaTeX specials: \_
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
Pigengene-package  325.748  1.088 326.766
one.step.pigengene 322.277  0.962 323.442
get.enriched.pw     98.598  4.632 103.399
module.heatmap      49.966  1.120  51.072
make.filter         26.531  0.756  27.288
apply.filter        25.015  0.100  25.116
compute.pigengene   23.770  0.164  23.935
plot.pigengene      23.245  0.127  23.373
pigengene           22.393  0.128  22.521
project.eigen       22.443  0.072  22.517
learn.bn            19.314  0.434  19.768
make.decision.tree  16.575  0.116  16.698
compact.tree        15.789  0.068  15.857
combine.networks    15.801  0.032  15.812
determine.modules   15.315  0.044  15.359
wgcna.one.step      14.267  0.044  14.311
gene.mapping         6.917  0.508  47.820
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘Pigengene_inference.Rnw’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/Pigengene.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Pigengene
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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)