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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:BgeeCall.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings BgeeCall_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/BgeeCall.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BgeeCall/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BgeeCall’ version ‘1.20.0’
* 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 ‘BgeeCall’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.2Mb
  sub-directories of 1Mb or more:
    extdata   8.7Mb
* 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
approachesMerging : <anonymous>: no visible global function definition
  for ‘p.adjust’
generate_calls_workflow: no visible binding for global variable
  ‘myUserMetadata’
generate_qValue: no visible global function definition for ‘approxfun’
generate_qValue: no visible global function definition for ‘integrate’
generate_qValue : calculate_qValue: no visible global function
  definition for ‘integrate’
generate_theoretical_pValue: no visible binding for global variable
  ‘abundance’
generate_theoretical_pValue: no visible binding for global variable
  ‘type’
generate_theoretical_pValue: no visible global function definition for
  ‘pnorm’
merging_libraries: no visible binding for global variable ‘read.delim’
should_ignore_tx_version: no visible global function definition for
  ‘complete.cases’
Undefined global functions or variables:
  abundance approxfun complete.cases integrate myUserMetadata p.adjust
  pnorm read.delim type
Consider adding
  importFrom("stats", "approxfun", "complete.cases", "integrate",
             "p.adjust", "pnorm")
  importFrom("utils", "read.delim")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) list_bgee_ref_intergenic_species.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) list_bgee_ref_intergenic_species.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) list_bgee_ref_intergenic_species.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) list_bgee_ref_intergenic_species.Rd:26: Lost braces in \itemize; meant \describe ?
* 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 ‘BgeeCall-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: generate_presence_absence
> ### Title: Generate presence absence
> ### Aliases: generate_presence_absence
> 
> ### ** Examples
> 
> {
+ # this example reuse data present in the directory 'extdata' of the package.
+ user <- new('UserMetadata', working_path = system.file('extdata', 
+ package = 'BgeeCall'), species_id = '6239', rnaseq_lib_path = system.file(
+ 'extdata', 'SRX099901_subset', package = 'BgeeCall'), 
+ annotation_name = 'WBcel235_84', simple_arborescence = TRUE)
+ calls_output <- generate_presence_absence(myUserMetadata = user)
+ 
+ #
+ }
Querying Bgee to get intergenic release information...
trying URL 'https://www.bgee.org/ftp/intergenic/1.0/ref_intergenic/6239_intergenic.fa.gz'
Content type 'application/x-gzip' length 4054193 bytes (3.9 MB)
==================================================
downloaded 3.9 MB

Note: importing `abundance.h5` is typically faster than `abundance.tsv`
reading in files with read.delim (install 'readr' package for speed up)
1 
* 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:
  Expectation did not fail
  ── Error ('test_transcriptToGene.R:33:3'): test creation of transcript to gene file ──
  Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'nrow': object 'txToGene' not found
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(nrow(txToGene), 4278) at test_transcriptToGene.R:33:3
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─base::nrow(txToGene)
   5. └─base::.handleSimpleError(...)
   6.   └─base (local) h(simpleError(msg, call))
  
  [ 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/BgeeCall.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL BgeeCall
###
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* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘BgeeCall’ ...
** 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 (BgeeCall)

R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.

> library(testthat)
> library(BgeeCall)
> 
> Sys.setenv("R_TESTS" = "")
> test_check("BgeeCall")
trying URL 'https://www.bgee.org/ftp/intergenic/0.1/ref_intergenic/6239_intergenic.fa.gz'
Content type 'application/x-gzip' length 4420457 bytes (4.2 MB)
==================================================
downloaded 4.2 MB

trying URL 'https://www.bgee.org/ftp/intergenic/0.1/ref_intergenic/6239_intergenic.fa.gz'
Content type 'application/x-gzip' length 4420457 bytes (4.2 MB)
==================================================
downloaded 4.2 MB

trying URL 'https://www.bgee.org/ftp/intergenic/0.1/ref_intergenic/6239_intergenic.fa.gz'
Content type 'application/x-gzip' length 4420457 bytes (4.2 MB)
==================================================
downloaded 4.2 MB

trying URL 'https://www.bgee.org/ftp/intergenic/0.1/ref_intergenic/6239_intergenic.fa.gz'
Content type 'application/x-gzip' length 4420457 bytes (4.2 MB)
==================================================
downloaded 4.2 MB

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 12 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_transcriptToGene.R:28:3'): test creation of transcript to gene file ──
Expectation did not fail
── Error ('test_transcriptToGene.R:33:3'): test creation of transcript to gene file ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'nrow': object 'txToGene' not found
Backtrace:
    ▆
 1. ├─testthat::expect_equal(nrow(txToGene), 4278) at test_transcriptToGene.R:33:3
 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. ├─base::nrow(txToGene)
 5. └─base::.handleSimpleError(...)
 6.   └─base (local) h(simpleError(msg, call))

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