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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ideal.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ideal_1.23.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ideal.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘ideal/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ideal’ version ‘1.23.0’
* 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 ‘ideal’ 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... NOTE

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* 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
ideal: no visible binding for '<<-' assignment to ‘ideal_env’
ideal : <anonymous>: no visible binding for global variable ‘airway’
ideal : <anonymous>: no visible binding for global variable ‘pvalue’
ideal : <anonymous>: no visible binding for global variable ‘baseMean’
ideal : <anonymous>: no visible binding for global variable ‘ideal_env’
Undefined global functions or variables:
  airway baseMean ideal_env pvalue
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
goseqTable      18.770  0.388  19.159
plot_ma          5.126  0.168   5.294
wrapup_for_iSEE  5.077  0.044   5.121
* 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:
   24.   │   └─bslib:::tabPanel_(title, ..., value = value, icon = icon)
   25.   │     └─htmltools::div(...)
   26.   │       └─rlang::dots_list(...)
   27.   ├─shiny::fluidRow(...)
   28.   │ └─htmltools::div(class = "row", ...)
   29.   │   └─rlang::dots_list(...)
   30.   ├─shiny::column(...)
   31.   │ └─htmltools::div(class = colClass, ...)
   32.   │   └─rlang::dots_list(...)
   33.   └─htmltools::includeMarkdown(...)
   34.     └─utils::packageVersion("markdown")
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  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 ...
  ‘ideal-usersguide.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/ideal.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ideal
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘ideal’ ...
** using staged installation
** R
** 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 (ideal)

R version 4.3.0 alpha (2023-04-03 r84154)
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(ideal)
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, setdiff, sort, 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 objects are masked from 'package:base':

    I, expand.grid, unname


Loading required package: SparseM

Attaching package: 'SparseM'

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

    backsolve


groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

Attaching package: 'topGO'

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

    members

Welcome to ideal v1.23.0

If you use ideal in your work, please cite:

Federico Marini, Jan Linke, Harald Binder
ideal: an R/Bioconductor package for Interactive Differential Expression Analysis
BMC Bioinformatics, 2020 - https://doi.org/10.1186/s12859-020-03819-5

> 
> test_check("ideal")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_shiny.R:11:3'): Shiny app is generated ─────────────────────────
<packageNotFoundError/error/condition>
Error in `packageVersion("markdown")`: there is no package called 'markdown'
Backtrace:
     ▆
  1. ├─testthat::expect_is(ideal(), "shiny.appobj") at test_shiny.R:11:2
  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. └─ideal::ideal()
  5.   ├─shinydashboard::dashboardPage(...)
  6.   │ └─shinydashboard:::tagAssert(body, type = "div", class = "content-wrapper")
  7.   ├─shinydashboard::dashboardBody(...)
  8.   │ ├─htmltools::div(...)
  9.   │ │ └─rlang::dots_list(...)
 10.   │ └─tags$section(class = "content", ...)
 11.   │   └─rlang::dots_list(...)
 12.   ├─htmltools::div(...)
 13.   │ └─rlang::dots_list(...)
 14.   ├─shinydashboard::tabBox(...)
 15.   │ └─shiny::tabsetPanel(..., id = id, selected = selected)
 16.   │   ├─shiny:::remove_first_class(...)
 17.   │   └─bslib (local) func(..., id = id, selected = selected, header = header, footer = footer)
 18.   │     └─bslib:::tabsetPanel_(...)
 19.   │       └─bslib:::buildTabset(...)
 20.   │         ├─bslib:::dropNulls(list2(...))
 21.   │         └─rlang::list2(...)
 22.   ├─shiny::tabPanel(...)
 23.   │ └─bslib::nav(title, ..., value = value, icon = icon)
 24.   │   └─bslib:::tabPanel_(title, ..., value = value, icon = icon)
 25.   │     └─htmltools::div(...)
 26.   │       └─rlang::dots_list(...)
 27.   ├─shiny::fluidRow(...)
 28.   │ └─htmltools::div(class = "row", ...)
 29.   │   └─rlang::dots_list(...)
 30.   ├─shiny::column(...)
 31.   │ └─htmltools::div(class = colClass, ...)
 32.   │   └─rlang::dots_list(...)
 33.   └─htmltools::includeMarkdown(...)
 34.     └─utils::packageVersion("markdown")

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted