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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:compSPOT.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings compSPOT_1.5.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/compSPOT.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 ‘compSPOT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘compSPOT’ version ‘1.5.0’
* package encoding: UTF-8
* 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 ‘compSPOT’ 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
compare_features : count_mutations_features: no visible binding for
  global variable ‘Sample’
compare_features : count_mutations_features: no visible binding for
  global variable ‘Chromosome’
count_groups: no visible binding for global variable ‘Group’
count_mutations: no visible binding for global variable ‘Sample’
count_mutations: no visible binding for global variable ‘Chromosome’
find_hotspots: no visible binding for global variable ‘percent’
plot_ecdf: no visible binding for global variable ‘Hotspot’
plot_ecdf: no visible binding for global variable ‘Mutation_Count’
plot_ecdf: no visible binding for global variable ‘Group’
plot_features: no visible global function definition for ‘na.omit’
plot_features: no visible binding for global variable ‘Count’
plot_sigspot: no visible binding for global variable ‘percent’
plot_sigspot: no visible binding for global variable ‘number’
plot_sigspot: no visible binding for global variable ‘Label’
plot_sigspot: no visible binding for global variable ‘type’
plot_sigspot: no visible binding for global variable ‘Count’
plot_sigspot: no visible binding for global variable ‘Group’
plot_spot: no visible binding for global variable ‘Mutation_Count’
plot_spot: no visible binding for global variable ‘Hotspot’
plot_spot: no visible binding for global variable ‘Group’
region_counter: no visible binding for global variable ‘Sample’
region_counter: no visible binding for global variable ‘Chromosome’
spot_rank: no visible binding for global variable ‘Chromosome’
Undefined global functions or variables:
  Chromosome Count Group Hotspot Label Mutation_Count Sample na.omit
  number percent type
Consider adding
  importFrom("stats", "na.omit")
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
compare_groups 70.579  1.215  71.688
find_hotspots   8.973  0.108   9.081
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/compSPOT.Rcheck/00check.log’
for details.