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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenVisR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenVisR_1.45.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.24-bioc/meat/GenVisR.Rcheck’
* using R version 4.6.0 Patched (2026-05-01 r89994)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-05-21 23:44:42 UTC
* using option ‘--no-vignettes’
* checking for file ‘GenVisR/DESCRIPTION’ ... OK
* this is package ‘GenVisR’ version ‘1.45.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘GenVisR’ 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 ... NOTE
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
buildWaterfallPlot,WaterfallData: no visible global function definition
  for ‘tail’
setTierTwo,data.table: no visible global function definition for ‘tail’
setTierTwo,data.table : a: no visible binding for global variable ‘tmp’
toLolliplot,GMS: no visible binding for global variable ‘missingINdex’
Undefined global functions or variables:
  missingINdex tail tmp
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) lohSpec.Rd:46: Lost braces; missing escapes or markup?
    46 | consisting of elements from the set {"M", "F"}. Used to suppress the plotting
       |                                     ^
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
geneViz 6.947  0.070   7.019
genCov  6.440  0.154   6.625
* 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:
  ── Error ('test-Lolliplot-class.R:818:5'): getData retrieves specified slot data correctly ──
  Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'getData': object 'Lolliplot.out' not found
  Backtrace:
      ▆
   1. ├─testthat::expect_s3_class(...) at test-Lolliplot-class.R:818:5
   2. │ └─testthat::quasi_label(enquo(object))
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─GenVisR::getData(Lolliplot.out, index = 1)
   5. └─base::.handleSimpleError(...)
   6.   └─base (local) h(simpleError(msg, call))
  
  [ FAIL 7 | WARN 4 | SKIP 46 | PASS 437 ]
  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: 1 ERROR, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.24-bioc/meat/GenVisR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GenVisR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘GenVisR’ ...
** this is package ‘GenVisR’ version ‘1.45.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (GenVisR)

R version 4.6.0 Patched (2026-05-01 r89994) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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(GenVisR)
> 
> test_check("GenVisR")
Error : Your query has been redirected to https://status.ensembl.org indicating this Ensembl service is currently unavailable.
Look at ?useEnsembl for details on how to try a mirror site.
Saving _problems/test-Lolliplot-class-80.R
Saving _problems/test-Lolliplot-class-116.R
Saving _problems/test-Lolliplot-class-124.R
Saving _problems/test-Lolliplot-class-140.R
Saving _problems/test-Lolliplot-class-768.R
Saving _problems/test-Lolliplot-class-791.R
Saving _problems/test-Lolliplot-class-818.R
[ FAIL 7 | WARN 4 | SKIP 46 | PASS 437 ]

══ Skipped tests (46) ══════════════════════════════════════════════════════════
• mart recieved try-error (45): 'test-Lolliplot-class.R:68:5',
  'test-Lolliplot-class.R:74:5', 'test-Lolliplot-class.R:97:5',
  'test-Lolliplot-class.R:151:5', 'test-Lolliplot-class.R:160:5',
  'test-Lolliplot-class.R:181:5', 'test-Lolliplot-class.R:189:5',
  'test-Lolliplot-class.R:201:5', 'test-Lolliplot-class.R:207:5',
  'test-Lolliplot-class.R:213:5', 'test-Lolliplot-class.R:237:5',
  'test-Lolliplot-class.R:254:5', 'test-Lolliplot-class.R:265:5',
  'test-Lolliplot-class.R:290:5', 'test-Lolliplot-class.R:296:5',
  'test-Lolliplot-class.R:308:5', 'test-Lolliplot-class.R:315:5',
  'test-Lolliplot-class.R:322:5', 'test-Lolliplot-class.R:329:5',
  'test-Lolliplot-class.R:349:5', 'test-Lolliplot-class.R:368:5',
  'test-Lolliplot-class.R:386:5', 'test-Lolliplot-class.R:395:5',
  'test-Lolliplot-class.R:404:5', 'test-Lolliplot-class.R:412:5',
  'test-Lolliplot-class.R:428:5', 'test-Lolliplot-class.R:434:5',
  'test-Lolliplot-class.R:443:5', 'test-Lolliplot-class.R:452:5',
  'test-Lolliplot-class.R:465:5', 'test-Lolliplot-class.R:477:5',
  'test-Lolliplot-class.R:490:5', 'test-Lolliplot-class.R:498:5',
  'test-Lolliplot-class.R:509:5', 'test-Lolliplot-class.R:522:5',
  'test-Lolliplot-class.R:545:5', 'test-Lolliplot-class.R:580:5',
  'test-Lolliplot-class.R:587:5', 'test-Lolliplot-class.R:660:5',
  'test-Lolliplot-class.R:669:5', 'test-Lolliplot-class.R:681:5',
  'test-Lolliplot-class.R:693:5', 'test-Lolliplot-class.R:712:5',
  'test-Lolliplot-class.R:746:5', 'test-Lolliplot-class.R:752:5'
• mart recieved try-error, biomart is possibly down or there is no internet
  connection. (1): 'test-Lolliplot-class.R:62:5'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-Lolliplot-class.R:80:5'): retreiveMart works in verbose mode ───
Error: Your query has been redirected to https://status.ensembl.org indicating this Ensembl service is currently unavailable.
Look at ?useEnsembl for details on how to try a mirror site.
Backtrace:
     ▆
  1. ├─testthat::expect_message(...) at test-Lolliplot-class.R:80:5
  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. ├─GenVisR:::retrieveMart(...)
  7. └─GenVisR:::retrieveMart(...)
  8.   └─GenVisR (local) .local(object, ...)
  9.     └─biomaRt::useMart("ENSEMBL_MART_ENSEMBL", host = host)
 10.       └─biomaRt:::.useMart(...)
 11.         └─biomaRt:::.listMarts(...)
── Error ('test-Lolliplot-class.R:113:5'): annotateGene warns if transcript is not a character ──
Error in `eval(code, test_env)`: object 'retrieveMart.out' not found
Backtrace:
     ▆
  1. ├─testthat::expect_warning(...) at test-Lolliplot-class.R:113:5
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. ├─GenVisR:::annotateGene(...)
  7. └─GenVisR:::annotateGene(...)
  8.   └─GenVisR (local) .local(object, ...)
  9.     └─biomaRt::getBM(...)
 10.       └─biomaRt:::martCheck(mart)
── Error ('test-Lolliplot-class.R:121:5'): annotateGene warns if more than 1 element is supplied to transcript ──
Error in `eval(code, test_env)`: object 'retrieveMart.out' not found
Backtrace:
     ▆
  1. ├─testthat::expect_warning(...) at test-Lolliplot-class.R:121:5
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. ├─GenVisR:::annotateGene(...)
  7. └─GenVisR:::annotateGene(...)
  8.   └─GenVisR (local) .local(object, ...)
  9.     └─biomaRt::getBM(...)
 10.       └─biomaRt:::martCheck(mart)
── Error ('test-Lolliplot-class.R:137:5'): annotateGene works in verbose mode ──
Error in `eval(code, test_env)`: object 'retrieveMart.out' not found
Backtrace:
     ▆
  1. ├─testthat::expect_message(...) at test-Lolliplot-class.R:137:5
  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. ├─GenVisR:::annotateGene(...)
  7. └─GenVisR:::annotateGene(...)
  8.   └─GenVisR (local) .local(object, ...)
  9.     └─biomaRt::getBM(...)
 10.       └─biomaRt:::martCheck(mart)
── Error ('test-Lolliplot-class.R:768:5'): Lolliplot constructor outputs a S4 class object ──
Error in `eval(code, test_env)`: object 'Lolliplot.out' not found
Backtrace:
    ▆
 1. └─testthat::expect_s4_class(Lolliplot.out, "Lolliplot") at test-Lolliplot-class.R:768:5
 2.   └─testthat::quasi_label(enquo(object))
 3.     └─rlang::eval_bare(expr, quo_get_env(quo))
── Error ('test-Lolliplot-class.R:791:5'): getGrob successfully retrieves grob objects ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'getGrob': object 'Lolliplot.out' not found
Backtrace:
    ▆
 1. ├─testthat::expect_s3_class(...) at test-Lolliplot-class.R:791:5
 2. │ └─testthat::quasi_label(enquo(object))
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. ├─GenVisR::getGrob(Lolliplot.out, index = 1)
 5. └─base::.handleSimpleError(...)
 6.   └─base (local) h(simpleError(msg, call))
── Error ('test-Lolliplot-class.R:818:5'): getData retrieves specified slot data correctly ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'getData': object 'Lolliplot.out' not found
Backtrace:
    ▆
 1. ├─testthat::expect_s3_class(...) at test-Lolliplot-class.R:818:5
 2. │ └─testthat::quasi_label(enquo(object))
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. ├─GenVisR::getData(Lolliplot.out, index = 1)
 5. └─base::.handleSimpleError(...)
 6.   └─base (local) h(simpleError(msg, call))

[ FAIL 7 | WARN 4 | SKIP 46 | PASS 437 ]
Error:
! Test failures.
Execution halted