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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:Uniquorn.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings Uniquorn_2.29.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/Uniquorn.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘Uniquorn/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Uniquorn’ version ‘2.29.0’
* 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 ... INFO
  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 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
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 ... ERROR
Running examples in ‘Uniquorn-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_custom_vcf_to_database
> ### Title: add_custom_vcf_to_database This function adds the variants of
> ###   parsed custom CCLs to a monet DB instance
> ### Aliases: add_custom_vcf_to_database
> 
> ### ** Examples
> 
> HT29_vcf_file = system.file("extdata/HT29_TEST.vcf", package = "Uniquorn");
> add_custom_vcf_to_database(
+     vcf_input_files = HT29_vcf_file,
+     library_name = "CELLMINER",
+     ref_gen = "GRCH37",
+     n_threads = 1,
+     test_mode = TRUE
+ )
Sample: HT29_TEST, Library: CELLMINER
Loading required namespace: GenomeInfoDb
Failed with error:  ‘there is no package called ‘GenomeInfoDb’’
Error in .requirePackage(package) : 
  unable to load required package ‘GenomeInfoDb’
Calls: add_custom_vcf_to_database ... vapply -> FUN -> is -> getClassDef -> .requirePackage
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    9.     └─GenomicRanges::findOverlaps(...)
   10.       └─GenomicRanges (local) .local(query, subject, maxgap, minoverlap, type, select, ...)
   11.         └─GenomicRanges:::findOverlaps_GNCList(...)
   12.           ├─base::merge(seqinfo(query), seqinfo(subject))
   13.           └─Seqinfo::merge(seqinfo(query), seqinfo(subject))
   14.             └─Seqinfo:::.merge_Seqinfo_objects(x, y, ...)
   15.               └─base::vapply(args, function(arg) is(arg, class(x)), logical(1))
   16.                 └─Seqinfo (local) FUN(X[[i]], ...)
   17.                   └─methods::is(arg, class(x))
   18.                     └─methods::getClassDef(...)
   19.                       └─methods:::.requirePackage(package)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 12 ]
  Error: Test failures
  Execution halted
* 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 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/Uniquorn.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL Uniquorn
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘Uniquorn’ ...
** this is package ‘Uniquorn’ version ‘2.29.0’
** 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 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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")
Failed with error:  'there is no package called 'GenomeInfoDb''
Failed with error:  'there is no package called 'GenomeInfoDb''
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 12 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_b_identification.R:5:5'): identification of test data returns correct results ──
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. └─Uniquorn::identify_vcf_file(...) at test_b_identification.R:5:5
  2.   └─Uniquorn:::match_query_ccl_to_database(...)
  3.     ├─GenomicRanges::findOverlaps(...)
  4.     └─GenomicRanges::findOverlaps(...)
  5.       └─GenomicRanges (local) .local(query, subject, maxgap, minoverlap, type, select, ...)
  6.         └─GenomicRanges:::findOverlaps_GNCList(...)
  7.           ├─base::merge(seqinfo(query), seqinfo(subject))
  8.           └─Seqinfo::merge(seqinfo(query), seqinfo(subject))
  9.             └─Seqinfo:::.merge_Seqinfo_objects(x, y, ...)
 10.               └─base::vapply(args, function(arg) is(arg, class(x)), logical(1))
 11.                 └─Seqinfo (local) FUN(X[[i]], ...)
 12.                   └─methods::is(arg, class(x))
 13.                     └─methods::getClassDef(class1)
 14.                       └─methods:::.requirePackage(package)
── Error ('test_c_remove_add.R:7:5'): adding and removing a custom Cancer Cell Line works succesfully ──
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─testthat::expect_message(...) at test_c_remove_add.R:7:5
  2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. └─Uniquorn::add_custom_vcf_to_database(...)
  7.   └─Uniquorn:::parse_vcf_query_into_db(...)
  8.     ├─IRanges::findOverlaps(...)
  9.     └─GenomicRanges::findOverlaps(...)
 10.       └─GenomicRanges (local) .local(query, subject, maxgap, minoverlap, type, select, ...)
 11.         └─GenomicRanges:::findOverlaps_GNCList(...)
 12.           ├─base::merge(seqinfo(query), seqinfo(subject))
 13.           └─Seqinfo::merge(seqinfo(query), seqinfo(subject))
 14.             └─Seqinfo:::.merge_Seqinfo_objects(x, y, ...)
 15.               └─base::vapply(args, function(arg) is(arg, class(x)), logical(1))
 16.                 └─Seqinfo (local) FUN(X[[i]], ...)
 17.                   └─methods::is(arg, class(x))
 18.                     └─methods::getClassDef(...)
 19.                       └─methods:::.requirePackage(package)

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 12 ]
Error: Test failures
Execution halted