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### Running command:
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###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings Pigengene_1.28.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/Pigengene.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Pigengene/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Pigengene’ version ‘1.28.0’
* 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 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 loading without being on the library search path ... 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 ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
one.step.pigengene 332.852  1.143 334.857
Pigengene-package  322.569  0.882 324.087
get.enriched.pw     90.917  2.499  93.814
module.heatmap      49.139  0.287  49.532
make.filter         28.449  0.072  28.580
apply.filter        26.860  0.092  26.991
project.eigen       24.447  0.203  24.695
plot.pigengene      24.406  0.116  24.565
pigengene           23.956  0.171  24.174
compute.pigengene   23.147  0.056  23.232
learn.bn            21.384  0.066  21.488
combine.networks    17.830  0.055  17.910
determine.modules   17.215  0.004  17.252
wgcna.one.step      16.405  0.016  16.454
compact.tree        16.296  0.096  16.423
make.decision.tree  16.105  0.072  16.208
gene.mapping         6.651  0.339  18.302
* 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
  ‘/home/biocbuild/bbs-3.18-bioc/meat/Pigengene.Rcheck/00check.log’
for details.