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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BgeeDB.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BgeeDB_2.32.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BgeeDB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BgeeDB’ version ‘2.32.0’
* 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 ‘BgeeDB’ can be installed ... OK
* checking installed package size ... OK
* 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 ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘BgeeDB-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Bgee-class
> ### Title: Bgee Reference Class
> ### Aliases: Bgee-class Bgee
> 
> ### ** Examples
> 
> {
+  bgee <- Bgee$new(species = "Mus_musculus", dataType = "rna_seq")
+  bgee <- Bgee$new(species = "Mus_musculus")
+ }

Querying Bgee to get release information...

WARNING: BgeeDB could not access Bgee releases information from the internet, but a release information file was found in the download directory /Users/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck. This release file will be used, but be warned that it may not be up to date!
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  line 6 did not have 21 elements
Calls: <Anonymous> ... initialize -> initialize -> <Anonymous> -> read.table -> scan
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:
      multi.line = FALSE, comment.char = comment.char, allowEscapes = allowEscapes, 
      flush = flush, encoding = encoding, skipNul = skipNul)`: line 6 did not have 21 elements
  Backtrace:
      ▆
   1. └─Bgee$new(species = "Bos_taurus", dataType = "rna_seq") at test_topAnat.R:5:3
   2.   └─methods::new(def, ...)
   3.     ├─methods::initialize(value, ...)
   4.     └─methods::initialize(value, ...)
   5.       └─.Object$initialize(...)
   6.         └─utils::read.table(...)
   7.           └─base::scan(...)
  
  [ FAIL 7 | WARN 0 | SKIP 0 | PASS 0 ]
  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
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BgeeDB
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘BgeeDB’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package can be loaded from final location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package keeps a record of temporary installation path
* DONE (BgeeDB)

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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(BgeeDB)
Loading required package: topGO
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: graph
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname


Loading required package: SparseM

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

Attaching package: 'topGO'

The following object is masked from 'package:IRanges':

    members

Loading required package: tidyr

Attaching package: 'tidyr'

The following object is masked from 'package:S4Vectors':

    expand

The following object is masked from 'package:testthat':

    matches

> 
> Sys.setenv("R_TESTS" = "")
> test_check("BgeeDB")

Querying Bgee to get release information...

WARNING: BgeeDB could not access Bgee releases information from the internet, but a release information file was found in the download directory /Users/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat. This release file will be used, but be warned that it may not be up to date!

Querying Bgee to get release information...

WARNING: BgeeDB could not access Bgee releases information from the internet, but a release information file was found in the download directory /Users/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat. This release file will be used, but be warned that it may not be up to date!

Querying Bgee to get release information...

Querying Bgee to get release information...

WARNING: BgeeDB could not access Bgee releases information from the internet, but a release information file was found in the download directory /Users/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat. This release file will be used, but be warned that it may not be up to date!

Querying Bgee to get release information...

WARNING: BgeeDB could not access Bgee releases information from the internet, but a release information file was found in the download directory /Users/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat. This release file will be used, but be warned that it may not be up to date!

Querying Bgee to get release information...

WARNING: BgeeDB could not access Bgee releases information from the internet, but a release information file was found in the download directory /Users/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat. This release file will be used, but be warned that it may not be up to date!

Querying Bgee to get release information...

WARNING: BgeeDB could not access Bgee releases information from the internet, but a release information file was found in the download directory /Users/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat. This release file will be used, but be warned that it may not be up to date!
[ FAIL 7 | WARN 0 | SKIP 0 | PASS 0 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_format_data.R:5:3'): Formatting gene expression files ──────────
Error in `scan(file = file, what = what, sep = sep, quote = quote, dec = dec, 
    nmax = nrows, skip = 0, na.strings = na.strings, quiet = TRUE, 
    fill = fill, strip.white = strip.white, blank.lines.skip = blank.lines.skip, 
    multi.line = FALSE, comment.char = comment.char, allowEscapes = allowEscapes, 
    flush = flush, encoding = encoding, skipNul = skipNul)`: line 6 did not have 21 elements
Backtrace:
    ▆
 1. └─Bgee$new(species = "Mus_musculus", dataType = "rna_seq") at test_format_data.R:5:3
 2.   └─methods::new(def, ...)
 3.     ├─methods::initialize(value, ...)
 4.     └─methods::initialize(value, ...)
 5.       └─.Object$initialize(...)
 6.         └─utils::read.table(...)
 7.           └─base::scan(...)
── Error ('test_list_annotation_output.R:5:3'): Annotation files ───────────────
Error in `scan(file = file, what = what, sep = sep, quote = quote, dec = dec, 
    nmax = nrows, skip = 0, na.strings = na.strings, quiet = TRUE, 
    fill = fill, strip.white = strip.white, blank.lines.skip = blank.lines.skip, 
    multi.line = FALSE, comment.char = comment.char, allowEscapes = allowEscapes, 
    flush = flush, encoding = encoding, skipNul = skipNul)`: line 6 did not have 21 elements
Backtrace:
    ▆
 1. └─Bgee$new(species = "Mus_musculus", dataType = "rna_seq") at test_list_annotation_output.R:5:3
 2.   └─methods::new(def, ...)
 3.     ├─methods::initialize(value, ...)
 4.     └─methods::initialize(value, ...)
 5.       └─.Object$initialize(...)
 6.         └─utils::read.table(...)
 7.           └─base::scan(...)
── Error ('test_listspecies_output.R:4:3'): Distinct species ───────────────────
Error in `scan(file = file, what = what, sep = sep, quote = quote, dec = dec, 
    nmax = nrows, skip = 0, na.strings = na.strings, quiet = TRUE, 
    fill = fill, strip.white = strip.white, blank.lines.skip = blank.lines.skip, 
    multi.line = FALSE, comment.char = comment.char, allowEscapes = allowEscapes, 
    flush = flush, encoding = encoding, skipNul = skipNul)`: line 6 did not have 21 elements
Backtrace:
    ▆
 1. └─BgeeDB::listBgeeSpecies(release = "14_2") at test_listspecies_output.R:4:3
 2.   └─BgeeDB:::.getBgeeRelease()
 3.     └─utils::read.table("release.tsv", header = TRUE, sep = "\t")
 4.       └─base::scan(...)
── Error ('test_loadTopAnatData.R:5:3'): Loading of topAnatData files is working ──
Error in `scan(file = file, what = what, sep = sep, quote = quote, dec = dec, 
    nmax = nrows, skip = 0, na.strings = na.strings, quiet = TRUE, 
    fill = fill, strip.white = strip.white, blank.lines.skip = blank.lines.skip, 
    multi.line = FALSE, comment.char = comment.char, allowEscapes = allowEscapes, 
    flush = flush, encoding = encoding, skipNul = skipNul)`: line 6 did not have 21 elements
Backtrace:
    ▆
 1. └─Bgee$new(species = "Bos_taurus", dataType = "rna_seq") at test_loadTopAnatData.R:5:3
 2.   └─methods::new(def, ...)
 3.     ├─methods::initialize(value, ...)
 4.     └─methods::initialize(value, ...)
 5.       └─.Object$initialize(...)
 6.         └─utils::read.table(...)
 7.           └─base::scan(...)
── Error ('test_loading_data_Bgee.R:5:3'): Gene expression files ───────────────
Error in `scan(file = file, what = what, sep = sep, quote = quote, dec = dec, 
    nmax = nrows, skip = 0, na.strings = na.strings, quiet = TRUE, 
    fill = fill, strip.white = strip.white, blank.lines.skip = blank.lines.skip, 
    multi.line = FALSE, comment.char = comment.char, allowEscapes = allowEscapes, 
    flush = flush, encoding = encoding, skipNul = skipNul)`: line 6 did not have 21 elements
Backtrace:
    ▆
 1. └─Bgee$new(species = "Drosophila_simulans", dataType = "rna_seq") at test_loading_data_Bgee.R:5:3
 2.   └─methods::new(def, ...)
 3.     ├─methods::initialize(value, ...)
 4.     └─methods::initialize(value, ...)
 5.       └─.Object$initialize(...)
 6.         └─utils::read.table(...)
 7.           └─base::scan(...)
── Error ('test_loading_separate_experiment.R:5:3'): Single experiment gene expression files ──
Error in `scan(file = file, what = what, sep = sep, quote = quote, dec = dec, 
    nmax = nrows, skip = 0, na.strings = na.strings, quiet = TRUE, 
    fill = fill, strip.white = strip.white, blank.lines.skip = blank.lines.skip, 
    multi.line = FALSE, comment.char = comment.char, allowEscapes = allowEscapes, 
    flush = flush, encoding = encoding, skipNul = skipNul)`: line 6 did not have 21 elements
Backtrace:
    ▆
 1. └─Bgee$new(species = "Mus_musculus", dataType = "rna_seq") at test_loading_separate_experiment.R:5:3
 2.   └─methods::new(def, ...)
 3.     ├─methods::initialize(value, ...)
 4.     └─methods::initialize(value, ...)
 5.       └─.Object$initialize(...)
 6.         └─utils::read.table(...)
 7.           └─base::scan(...)
── Error ('test_topAnat.R:5:3'): Creating the topAnat object is working ────────
Error in `scan(file = file, what = what, sep = sep, quote = quote, dec = dec, 
    nmax = nrows, skip = 0, na.strings = na.strings, quiet = TRUE, 
    fill = fill, strip.white = strip.white, blank.lines.skip = blank.lines.skip, 
    multi.line = FALSE, comment.char = comment.char, allowEscapes = allowEscapes, 
    flush = flush, encoding = encoding, skipNul = skipNul)`: line 6 did not have 21 elements
Backtrace:
    ▆
 1. └─Bgee$new(species = "Bos_taurus", dataType = "rna_seq") at test_topAnat.R:5:3
 2.   └─methods::new(def, ...)
 3.     ├─methods::initialize(value, ...)
 4.     └─methods::initialize(value, ...)
 5.       └─.Object$initialize(...)
 6.         └─utils::read.table(...)
 7.           └─base::scan(...)

[ FAIL 7 | WARN 0 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted