##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GraphPAC.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GraphPAC_1.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/GraphPAC.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 ‘GraphPAC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GraphPAC’ version ‘1.48.0’
* 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 ‘GraphPAC’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
Packages in Depends field not imported from:
  ‘RMallow’ ‘TSP’ ‘iPAC’ ‘igraph’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Find.TSP.Path: no visible global function definition for ‘dist’
Find.TSP.Path: no visible global function definition for ‘ATSP’
Find.TSP.Path: no visible global function definition for ‘insert_dummy’
Find.TSP.Path: no visible global function definition for ‘solve_TSP’
Find.TSP.Path: no visible global function definition for ‘cut_tour’
GraphClust: no visible global function definition for ‘graph.empty’
GraphClust: no visible global function definition for ‘V’
GraphClust: no visible global function definition for ‘V<-’
GraphClust: no visible global function definition for ‘add.edges’
GraphClust: no visible global function definition for ‘nmc’
Plot.Protein: no visible global function definition for ‘heat.colors’
Plot.Protein: no visible global function definition for ‘vcount’
Plot.Protein: no visible global function definition for ‘gray’
Plot.Protein: no visible global function definition for ‘topo.colors’
Plot.Protein: no visible global function definition for ‘cm.colors’
Plot.Protein: no visible global function definition for ‘V’
Plot.Protein: no visible global function definition for ‘tkplot’
Plot.Protein: no visible binding for global variable ‘layout.circle’
Undefined global functions or variables:
  ATSP V V<- add.edges cm.colors cut_tour dist graph.empty gray
  heat.colors insert_dummy layout.circle nmc solve_TSP tkplot
  topo.colors vcount
Consider adding
  importFrom("grDevices", "cm.colors", "gray", "heat.colors",
             "topo.colors")
  importFrom("stats", "dist")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) Plot.Protein.Rd:33: Lost braces
    33 | This function is based on the ``tkplot" function in \emph{igraph}. Please see the documentation for that package for the necessary requirements. Special thanks to Dr. G\'{a}bor Cs\'{a}rdi (creator of the \emph{igraph} package) for his help.
       |                                                                                                                                                                           ^
checkRd: (-1) Plot.Protein.Rd:33: Lost braces
    33 | This function is based on the ``tkplot" function in \emph{igraph}. Please see the documentation for that package for the necessary requirements. Special thanks to Dr. G\'{a}bor Cs\'{a}rdi (creator of the \emph{igraph} package) for his help.
       |                                                                                                                                                                                      ^
* 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
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
Find.TSP.Path 3.456   0.15   5.827
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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: 4 NOTEs
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/GraphPAC.Rcheck/00check.log’
for details.