##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Pigengene_1.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/Pigengene.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘Pigengene/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Pigengene’ version ‘1.31.0’
* 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 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
one.step.pigengene 79.905  0.539  80.443
Pigengene-package  75.354  1.012  76.277
get.enriched.pw    67.152  3.184  70.401
module.heatmap     35.205  0.271  35.464
learn.bn           20.463  0.156  20.619
make.filter        15.433  0.067  15.501
apply.filter       13.852  0.159  14.012
combine.networks   13.388  0.015  13.382
determine.modules  13.269  0.033  13.302
wgcna.one.step     12.175  0.016  12.191
make.decision.tree 10.545  0.135  10.681
compact.tree       10.085  0.056  10.141
compute.pigengene   6.867  0.116   6.983
pigengene           6.825  0.092   6.917
gene.mapping        6.289  0.343  12.520
plot.pigengene      6.562  0.027   6.590
project.eigen       6.241  0.060   6.301
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/Pigengene.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL Pigengene
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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)