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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:cpvSNP.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings cpvSNP_1.39.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/cpvSNP.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* 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 ‘cpvSNP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cpvSNP’ version ‘1.39.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘cpvSNP’ 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' call to ‘GSEABase’ which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
assocPvalBySetPlot: no visible global function definition for ‘rgb’
assocPvalBySetPlot: no visible global function definition for ‘col2rgb’
assocPvalBySetPlot : <anonymous>: no visible global function definition
  for ‘density’
assocPvalBySetPlot: no visible global function definition for ‘legend’
assocPvalBySetPlot: no visible global function definition for ‘polygon’
assocPvalBySetPlot: no visible global function definition for ‘lines’
assocPvalBySetPlot: no visible global function definition for ‘points’
createArrayData: no visible global function definition for ‘GRanges’
createArrayData: no visible global function definition for ‘Rle’
createArrayData: no visible global function definition for ‘IRanges’
createArrayData: no visible global function definition for
  ‘elementMetadata<-’
geneToSNPList: no visible global function definition for ‘findOverlaps’
glossiMarginal: no visible global function definition for ‘pgamma’
plotPvals: no visible binding for global variable ‘df’
plotPvals: no visible binding for global variable ‘pval’
simulate_chisq: no visible global function definition for ‘rnorm’
vegasMarginal: no visible global function definition for ‘rbinom’
vegasMarginal: no visible global function definition for ‘qchisq’
vegasPrep: no visible global function definition for ‘elementMetadata’
show,VEGASResult: no visible global function definition for ‘var’
Undefined global functions or variables:
  GRanges IRanges Rle col2rgb density df elementMetadata
  elementMetadata<- findOverlaps legend lines pgamma points polygon
  pval qchisq rbinom rgb rnorm var
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
  importFrom("graphics", "legend", "lines", "points", "polygon")
  importFrom("stats", "density", "df", "pgamma", "qchisq", "rbinom",
             "rnorm", "var")
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 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
geneToSNPList 4.989  0.469   5.205
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/cpvSNP.Rcheck/00check.log’
for details.