Package: Uniquorn

Version: 2.6.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:Uniquorn.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings Uniquorn_2.6.0.tar.gz

StartedAt: 2020-04-15 03:37:11 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:42:02 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 291.3 seconds

RetCode: 0

Status:  OK

CheckDir: Uniquorn.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:Uniquorn.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings Uniquorn_2.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/Uniquorn.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Uniquorn/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Uniquorn’ version ‘2.6.0’
* 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 ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 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 global function definition for
  ‘fread’
parse_ccle_genotype_data: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
parse_ccle_genotype_data: no visible global function definition for
  ‘data.table’
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 global function definition for
  ‘fread’
parse_cosmic_genotype_data: no visible binding for global variable
  ‘position’
parse_cosmic_genotype_data: no visible global function definition for
  ‘data.table’
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 Index Tumor_Sample_Barcode ccls_all data.table fread
  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
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/Uniquorn.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL Uniquorn
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 21 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 20.888   0.536  21.527 

name	user	system	elapsed
add_custom_vcf_to_database	3.624	0.060	3.934
identify_vcf_file	0.720	0.012	0.763
initiate_canonical_databases	0.000	0.000	0.001
read_library_names	0.000	0.000	0.001
remove_ccls_from_database	1.176	0.008	1.185
remove_library_from_database	0.000	0.000	0.002
show_contained_ccls	0.008	0.004	0.011
show_contained_variants_for_ccl	0.116	0.000	0.116
show_contained_variants_in_library	0.06	0.00	0.06
show_which_ccls_contain_variant	0.092	0.004	0.098