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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Rcollectl.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Rcollectl_1.6.0.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rcollectl.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘Rcollectl/DESCRIPTION’ ... OK
* this is package ‘Rcollectl’ version ‘1.6.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rcollectl’ 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 loading without being on the library search path ... 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
plot_usage: no visible binding for global variable ‘tm’
plot_usage: no visible binding for global variable ‘value’
plot_usage: no visible binding for global variable ‘type’
Undefined global functions or variables:
  tm type value
* 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 ... ERROR
Running examples in ‘Rcollectl-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cl_timestamp
> ### Title: Functions to add time stamps to collectl output
> ### Aliases: cl_timestamp cl_timestamp_layer cl_timestamp_label
> 
> ### ** Examples
> 
> id <- cl_start() 
> Sys.sleep(2)
> cl_timestamp(id, "step1")
> Sys.sleep(2)
> Sys.sleep(2)
> cl_timestamp(id, "step2")
> Sys.sleep(2)
> Sys.sleep(2)
> cl_timestamp(id, "step3")
> Sys.sleep(2)
> cl_stop(id)
> path <- cl_result_path(id)
> plot_usage(cl_parse(path)) +
+   cl_timestamp_layer(path) +
+   cl_timestamp_label(path) +
+   ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90, vjust = 0.5, hjust=1))
Error in cl_parse(path) : length(inds) == 2 is not TRUE
Calls: plot_usage ... cpu_active -> data.frame -> as.POSIXct -> cl_parse -> stopifnot
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:
  > 
  > test_check("Rcollectl")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 7 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('tests.R:36:3'): it works ────────────────────────────────────────────
  Error in `cl_parse(targ)`: length(inds) == 2 is not TRUE
  Backtrace:
      ▆
   1. └─Rcollectl::cl_parse(targ) at tests.R:36:3
   2.   └─base::stopifnot(length(inds) == 2)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 7 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘Rcollectl.Rmd’ using rmarkdown

Quitting from lines 115-136 [lkts] (Rcollectl.Rmd)
Error: processing vignette 'Rcollectl.Rmd' failed with diagnostics:
length(inds) == 2 is not TRUE
--- failed re-building ‘Rcollectl.Rmd’

SUMMARY: processing the following file failed:
  ‘Rcollectl.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs, 2 NOTEs
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rcollectl.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL Rcollectl
###
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* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘Rcollectl’ ...
** 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 (Rcollectl)

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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(Rcollectl)
> 
> test_check("Rcollectl")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 7 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('tests.R:36:3'): it works ────────────────────────────────────────────
Error in `cl_parse(targ)`: length(inds) == 2 is not TRUE
Backtrace:
    ▆
 1. └─Rcollectl::cl_parse(targ) at tests.R:36:3
 2.   └─base::stopifnot(length(inds) == 2)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 7 ]
Error: Test failures
Execution halted