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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GenVisR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GenVisR_1.22.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/GenVisR.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenVisR/DESCRIPTION’ ... OK
* this is package ‘GenVisR’ version ‘1.22.1’
* 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 ‘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 R 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
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 tmp
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
Lolliplot-class 30.708  0.885  59.373
lolliplot       12.075  0.079  27.804
geneViz          9.134  0.177   9.370
cnFreq           7.712  0.040   7.764
genCov           7.178  0.374   7.684
cnSpec           5.383  0.019   5.413
* 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:
   20. │                       ├─DBI::dbGetQuery(con, sql)
   21. │                       └─DBI::dbGetQuery(con, sql)
   22. │                         └─DBI:::.local(conn, statement, ...)
   23. │                           ├─DBI::dbSendQuery(conn, statement, ...)
   24. │                           └─RSQLite::dbSendQuery(conn, statement, ...)
   25. │                             └─RSQLite:::.local(conn, statement, ...)
   26. │                               ├─methods::new(...)
   27. │                               │ ├─methods::initialize(value, ...)
   28. │                               │ └─methods::initialize(value, ...)
   29. │                               └─RSQLite:::result_create(conn@ptr, statement)
   30. └─dplyr::collect(., Inf)
  
  [ FAIL 1 | WARN 13 | SKIP 44 | PASS 607 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/GenVisR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GenVisR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘GenVisR’ ...
** 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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (44)

══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test-Lolliplot-class.R:376:5): (code run outside of `test_that()`) ───
Error: attempt to write a readonly database
Backtrace:
     █
  1. ├─GenVisR:::constructTranscriptData(...) test-Lolliplot-class.R:376:4
  2. ├─GenVisR:::constructTranscriptData(...)
  3. │ └─GenVisR:::.local(object, ...)
  4. │   └─biomaRt::getBM(...)
  5. │     └─BiocFileCache::BiocFileCache(cache, ask = FALSE)
  6. │       └─BiocFileCache:::.sql_create_db(bfc)
  7. │         └─BiocFileCache:::.sql_validate_version(bfc)
  8. │           └─BiocFileCache:::.sql_schema_version(bfc)
  9. │             ├─base::tryCatch(...)
 10. │             │ └─base:::tryCatchList(expr, classes, parentenv, handlers)
 11. │             ├─tbl(src, "metadata") %>% collect(Inf)
 12. │             ├─dplyr::tbl(src, "metadata")
 13. │             └─dbplyr:::tbl.src_dbi(src, "metadata")
 14. │               └─dbplyr::tbl_sql(c(subclass, "dbi"), src = src, from = from, ...)
 15. │                 ├─vars %||% dbplyr_query_fields(src$con, from)
 16. │                 └─dbplyr:::dbplyr_query_fields(src$con, from)
 17. │                   └─dbplyr:::dbplyr_fallback(con, "db_query_fields", ...)
 18. │                     ├─rlang::eval_bare(expr((!!fun)(con, ...)))
 19. │                     └─dbplyr:::db_query_fields.DBIConnection(con, ...)
 20. │                       ├─DBI::dbGetQuery(con, sql)
 21. │                       └─DBI::dbGetQuery(con, sql)
 22. │                         └─DBI:::.local(conn, statement, ...)
 23. │                           ├─DBI::dbSendQuery(conn, statement, ...)
 24. │                           └─RSQLite::dbSendQuery(conn, statement, ...)
 25. │                             └─RSQLite:::.local(conn, statement, ...)
 26. │                               ├─methods::new(...)
 27. │                               │ ├─methods::initialize(value, ...)
 28. │                               │ └─methods::initialize(value, ...)
 29. │                               └─RSQLite:::result_create(conn@ptr, statement)
 30. └─dplyr::collect(., Inf)

[ FAIL 1 | WARN 13 | SKIP 44 | PASS 607 ]
Error: Test failures
Execution halted