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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:Rcollectl.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings Rcollectl_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/Rcollectl.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘Rcollectl/DESCRIPTION’ ... OK
* this is package ‘Rcollectl’ version ‘1.10.0’
* 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))
Warning in readLines(path) : line 1 appears to contain an embedded nul
Warning in readLines(path) : line 9 appears to contain an embedded nul
Warning in readLines(path) : line 10 appears to contain an embedded nul
Warning in readLines(path) : line 13 appears to contain an embedded nul
Warning in readLines(path) : line 16 appears to contain an embedded nul
Warning in readLines(path) :
  incomplete final line found on '/tmp/RtmpQrmPqt/file115626576d2736-nebbiolo2-20251216.tab.gz'
Warning in grep("^####", full) :
  unable to translate '<8b>' to a wide string
Warning in grep("^####", full) : input string 1 is invalid
Warning in grep("^####", full) :
  unable to translate '9<bf>E<ff><b3>tY<95>E<db><ef><d2>$gU<99>><a7><f1>x<99><ce><fe>ɾ<de><d5>yU3<a9><8f>8V<c3>><df>LeIu_<94><f3>f<be><b3><a4><8a><bd>W<cd>R<d8>
W<dc>p<ce><d8>$Ni<d9><ce><ef><a4>B<cb><cd>oX9=<c3><c8>I}7<f9><b1>l<c7>6,Vl<d8>e^<c5><f2>)<c9><d9>u=?}E<ab...' to a wide string
Warning in grep("^####", full) : input string 2 is invalid
Warning in grep("^####", full) :
  unable to translate 'I<bf><b3>b<fa>K<ea>N;|:<b9><ec><e1><9c>}' to a wide string
Warning in grep("^####", full) : input string 3 is invalid
Warning in grep("^####", full) :
  unable to translate '<83><98>k<df>l4' to a wide string
Warning in grep("^####", full) : input string 4 is invalid
Warning in grep("^####", full) :
  unable to translate '<b7>V<f1><bf><b2><d5><de><fd><c5>i<89><bc><a4>(e7<e9><<b2>o<a6>ۯ<cb>X<fe><ad><af><d3>i<ec>DDc'<fd><9a><a4>U'^<96><bf><f7><8f><8b><fb><be>qR<c5>$<eb>;̲<de><c0>MQ<f5><ad>?<d7>qYm<ca><d7>}<f7><bc>*<d5><f1>2N[<fd><b4>z^+<a3><b2><98>nk<bf><d4>q<ad><8c...' to a wide string
Warning in grep("^####", full) : input string 5 is invalid
Warning in grep("^####", full) :
  unable to translate '<d9>l<b6>w' to a wide string
Warning in grep("^####", full) :
  unable to translate 'záV><c9><f9><ea><fc><ea>v%<80>¬<95>><96>1<b6><d2><e4>{R<f6><ad>'<f5>}+<9c>&<d3><ef>}<e3>$K<ee>Z<e9>*Y<b4>‡<bc><c8><d7><d2>E7<a6><98><cf><d3>n<a2><cf><fd>x<84><ea><ca>R<d6>^<90><b6><e1>	<b4><cb>|-<a9><bb>AgiY<fd><e8>&<c9>b<d2>u<f9><9c><d4><f9><...' to a wide string
Warning in grep("^####", full) :
  unable to translate 'S<a6><91><94>t!0#<bc>fRh&<b4><81>`<e9><b0>A|[
<f5>HIj<e4>%<cf>9<ad><b7><9e>ͥ<90><8a><9e>Z<a5><94><d5>LK<e1><85><c2>Q<a1><ad><d4>VS$L<af><83><91>Z7<b3>*+<a5><97>4<95><f2>|]5<8e>(<93><92><c3>)A<a6>P<e0><c9>qOk<a1>q<c1>[<bc>=<b3><9c>i<9a><87>3<cd...' to a wide string
Warning in grep("^####", full) :
  unable to translate '8XA<8b><8b>!\Z4<b8><87>=<ed>0[<80><b5>9<ef><9b>Y<8d><c0>X8<f8>'<b8><9a><85>J<be>F@<df><c3><ed><93><f0><de><db>Ւ<88><94>u<f6>Rd<8f><e6><90><fd>Hr<84>F`m<f8><ec><d1><d2>o<d0>V	<ac><81>%%<d1><ee>0Z<af><b0><bd><da><a7><84>ܡ<e5><b8>ohY<fa>u<8...' to a wide string
Warning in grep("^####", full) :
  unable to translate 'XL7<ac><d9>-<e8>{<90><cc>[<90><b0>3<f8>6<9e>	,<ae><86>CJ9<83>' to a wide string
Warning in grep("^####", full) :
  unable to translate ' e<af><b6>1	4<9b><97> ) <92>롸<b1><eb>6#<f7>h<b9>7k<94>$S
5' to a wide string
Warning in grep("^####", full) :
  unable to translate 'U<b4>lG<8b><d6>Z<b2><a1>%<f6>h<a1>9Dh!<e5>\<b0>;<b4>R<85>h<a1><8a>-<aa>' to a wide string
Warning in grep("^####", full) :
  unable to translate 'D<c6><cb><c6>Ie<b4><f1>VP<dd>Vt<b4>4<8a>6' to a wide string
Warning in grep("^####", full) :
  unable to translate '<ff><b2>B<aa>3ޒ' to a wide string
Warning in grep("^####", full) :
  unable to translate '<b8>THMsM<c0>m<97>qNF<f0><84><89>-V!<85><ea><82><ce><fd>X<9c><c2>D'<96><db><c5>%<f8>[<b8><bc><a6>9	n<a0><a1><ba>՟<96><86><ae>F<e1><a4>q~W<93>2t<a1>2<94>}8ڛ<c0><c2>^(<de><e2><d2>
w<84><c3><ca>9(<ac><8a><95><e7><bc>$<8d><a4><8a>.<84>V<9b><b...' to a wide string
Warning in grep("^####", full) :
  unable to translate 'Y<ab>w@)<de>f zSZIe<ca>H\S<a1><95>BN<ca>îR<b8><ac><82>B<f1>t9BE<81><bb><ad><b8><b2><a3><85><d8>#%<a9>R<89>~<9c>䢿t<fe><a2><a3><c9>v<f9>' to a wide string
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
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
cl_result_path 0.576  0.227   6.303
cl_stop        0.544  0.231   6.278
cl_start       0.553  0.219   6.275
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/Rcollectl.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL Rcollectl
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘Rcollectl’ ...
** this is package ‘Rcollectl’ version ‘1.10.0’
** 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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 0 | WARN 0 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
  5.339   0.695  15.495