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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:sitePath.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings sitePath_1.22.0.tar.gz
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* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/sitePath.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘sitePath/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sitePath’ version ‘1.22.0’
* package encoding: UTF-8
* 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 ‘sitePath’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* checking installed package size ... NOTE
  installed size is  7.5Mb
  sub-directories of 1Mb or more:
    extdata   1.3Mb
    libs      5.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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
.createSNPplot: no visible binding for global variable ‘Pos’
.createSNPplot: no visible binding for global variable ‘Accession’
.createSNPplot: no visible binding for global variable ‘SNP’
plot.fixationPath: no visible binding for global variable ‘branch’
plot.fixationPath: no visible binding for global variable ‘SNPs’
plot.fixationSites: no visible binding for global variable ‘group’
plot.fixationSites: no visible binding for global variable ‘branch’
plot.fixationSites: no visible binding for global variable ‘SNPs’
plot.parallelSites: no visible binding for global variable ‘branch’
plot.parallelSites: no visible binding for global variable ‘SNPs’
plot.sitePath: no visible binding for global variable ‘branch’
plot.sitePath: no visible binding for global variable ‘SNPs’
plotMutSites.lineagePath: no visible binding for global variable ‘node’
plotMutSites.paraFixSites: no visible binding for global variable
  ‘group’
plotMutSites.paraFixSites: no visible binding for global variable
  ‘branch’
plotMutSites.paraFixSites: no visible binding for global variable
  ‘SNPs’
plotSingleSite.parallelSites: no visible binding for global variable
  ‘branch’
plotSingleSite.parallelSites: no visible binding for global variable
  ‘SNPs’
Undefined global functions or variables:
  Accession Pos SNP SNPs branch group node
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
plotFunctions     10.926  0.009  12.314
plotSingleSite     6.528  0.010   7.448
plotParallelSites  5.431  0.004   6.546
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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/sitePath.Rcheck/00check.log’
for details.