##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MODA.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MODA_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/MODA.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘MODA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MODA’ version ‘1.34.0’
* 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 ‘MODA’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
MIcondition: no visible binding for global variable ‘pwd’
WeightedModulePartitionSpectral: no visible binding for global variable
  ‘indicator’
Undefined global functions or variables:
  indicator pwd
* checking Rd files ... NOTE
checkRd: (-1) WeightedModulePartitionAmoutain.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{power}{the power parameter of WGCNA, W_{ij}=|cor(x_i,x_j)|^pwr}
       |                                              ^
checkRd: (-1) WeightedModulePartitionHierarchical.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{power}{the power parameter of WGCNA, W_{ij}=|cor(x_i,x_j)|^power}
       |                                              ^
checkRd: (-1) WeightedModulePartitionLouvain.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{power}{the power parameter of WGCNA, W_{ij}=|cor(x_i,x_j)|^power}
       |                                              ^
checkRd: (-1) WeightedModulePartitionSpectral.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{power}{the power parameter of WGCNA, W_{ij}=|cor(x_i,x_j)|^power}
       |                                              ^
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ... OK
* checking package vignettes ... NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/MODA.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL MODA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘MODA’ ...
** this is package ‘MODA’ version ‘1.34.0’
** 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 (MODA)