##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:pathRender.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings pathRender_1.74.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/pathRender.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘pathRender/DESCRIPTION’ ... OK
* this is package ‘pathRender’ version ‘1.74.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'graph', 'Rgraphviz', 'RColorBrewer', 'cMAP', 'AnnotationDbi',
  'stats4'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘pathRender’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
graphcMAP: no visible binding for global variable ‘cMAPKEGGPATHWAY’
graphcMAP: no visible binding for global variable ‘cMAPCARTAPATHWAY’
graphcMAP: no visible binding for global variable ‘cMAPKEGGINTERACTION’
graphcMAP: no visible binding for global variable ‘cMAPKEGGMOLECULE’
graphcMAP: no visible binding for global variable
  ‘cMAPCARTAINTERACTION’
graphcMAP: no visible binding for global variable ‘cMAPCARTAMOLECULE’
plotExGraph: no visible global function definition for
  ‘colorRampPalette’
plotExGraph: no visible global function definition for ‘exprs’
quantizeByRow : <anonymous>: no visible global function definition for
  ‘quantile’
quantizeByRow: no visible global function definition for ‘featureNames’
quantizeByRow: no visible global function definition for ‘exprs<-’
quantizeByRow: no visible global function definition for ‘exprs’
quantizeByRow: no visible global function definition for
  ‘featureNames<-’
reduceES: no visible global function definition for ‘na.omit’
reduceES: no visible global function definition for ‘featureData<-’
reduceES: no visible global function definition for ‘exprs’
reduceES: no visible global function definition for ‘phenoData’
rendercMAPPathway: no visible binding for global variable
  ‘cMAPKEGGPATHWAY’
rendercMAPPathway: no visible binding for global variable
  ‘cMAPCARTAPATHWAY’
rendercMAPPathway: no visible binding for global variable
  ‘cMAPKEGGINTERACTION’
rendercMAPPathway: no visible binding for global variable
  ‘cMAPKEGGMOLECULE’
rendercMAPPathway: no visible binding for global variable
  ‘cMAPCARTAINTERACTION’
rendercMAPPathway: no visible binding for global variable
  ‘cMAPCARTAMOLECULE’
plot,coloredGraph-ANY: no visible global function definition for
  ‘palette’
Undefined global functions or variables:
  cMAPCARTAINTERACTION cMAPCARTAMOLECULE cMAPCARTAPATHWAY
  cMAPKEGGINTERACTION cMAPKEGGMOLECULE cMAPKEGGPATHWAY colorRampPalette
  exprs exprs<- featureData<- featureNames featureNames<- na.omit
  palette phenoData quantile
Consider adding
  importFrom("grDevices", "colorRampPalette", "palette")
  importFrom("stats", "na.omit", "quantile")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 2 NOTEs
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/pathRender.Rcheck/00check.log’
for details.

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


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘pathRender’ ...
** using staged installation
** R
** 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 (pathRender)