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### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:Uniquorn.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings Uniquorn_2.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/Uniquorn.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘Uniquorn/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Uniquorn’ version ‘2.22.0’
* 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 ‘Uniquorn’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.6Mb
  sub-directories of 1Mb or more:
    extdata   6.5Mb
* 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 R 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
add_p_q_values_statistics: no visible binding for '<<-' assignment to
  ‘sig_vec’
add_p_q_values_statistics: no visible binding for global variable
  ‘sig_vec’
create_bed_file: no visible binding for global variable ‘res_table’
create_bed_file: no visible binding for global variable ‘sim_list’
identify_vcf_file: no visible binding for global variable
  ‘vcf_fingerprint’
identify_vcf_file: no visible binding for global variable
  ‘output_file_xls’
init_and_load_identification: no visible global function definition for
  ‘tail’
parse_ccle_genotype_data: no visible binding for global variable
  ‘Cell_line’
parse_ccle_genotype_data: no visible binding for global variable ‘.SD’
parse_ccle_genotype_data: no visible binding for global variable
  ‘Index’
parse_cosmic_genotype_data: no visible binding for global variable
  ‘position’
parse_cosmic_genotype_data: no visible binding for global variable
  ‘.SD’
parse_cosmic_genotype_data: no visible binding for global variable
  ‘Index’
show_contained_ccls: no visible binding for '<<-' assignment to
  ‘ccls_all’
show_contained_ccls: no visible binding for global variable ‘ccls_all’
write_w0_and_split_w0_into_lower_weights: no visible binding for '<<-'
  assignment to ‘g_mat_exclude’
write_w0_and_split_w0_into_lower_weights: no visible binding for global
  variable ‘g_mat_exclude’
Undefined global functions or variables:
  .SD Cell_line Index ccls_all g_mat_exclude output_file_xls position
  res_table sig_vec sim_list tail vcf_fingerprint
Consider adding
  importFrom("utils", "tail")
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
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
add_custom_vcf_to_database 5.992    0.3   6.293
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘Uniquorn.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/Uniquorn.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL Uniquorn
###
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* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘Uniquorn’ ...
** 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 (Uniquorn)

R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> Sys.setenv(R_TESTS="")
> library("testthat")
> library("Uniquorn")
> 
> test_check("Uniquorn")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 21 ]
> 
> proc.time()
   user  system elapsed 
 20.337   0.922  21.248