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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BgeeCall.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BgeeCall_1.21.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/BgeeCall.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BgeeCall/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BgeeCall' version '1.21.0'
* 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 whether package 'BgeeCall' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.1Mb
  sub-directories of 1Mb or more:
    extdata   8.6Mb
* 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 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
setAnnotationFromFile     3.64   5.78   42.66
generate_presence_absence 5.25   0.35    7.98
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/BgeeCall.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL BgeeCall
###
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* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 0 | WARN 0 | SKIP 0 | PASS 15 ]
> 
> proc.time()
   user  system elapsed 
  27.76   14.14   52.23