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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_1.5.1.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rcollectl.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘1.5.1’
* 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 ... 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 7 appears to contain an embedded nul
Warning in readLines(path) : line 11 appears to contain an embedded nul
Warning in readLines(path) : line 13 appears to contain an embedded nul
Warning in readLines(path) :
  incomplete final line found on '/tmp/Rtmp0IKCge/file3d58ce727fa63c-teran2-20240912.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 ';Yd<99><97>Y<9f>1<f6><9b>>P<a2>';K<af><fd><aa><cf> }X<96><e9>"<87><dc>[<8d>'<f3><9c><f5><ae>XozXΗ<87><d7><f8><e0><e7>'38M3<af>&<91>{+<ed>41j<cc>`<fa>l<b1>*<c9>,}<95><be>Hr<c9><d8>i<e2><e7><8b>Fa]<8e><8b><d2>OB'a<a5><e1>V8<ab><b4>f<9f>$<97><9...' to a wide string
Warning in grep("^####", full) : input string 2 is invalid
Warning in grep("^####", full) :
  unable to translate 'k<ff><e6>)H1<c9>nҹg<9f>:<b7>W<be><f8>><88><97><e9><d8>7"b<af><91>~OҲϋ<bf><db>׋i<db>8,}<92><b5>&Yk<e0>fQ<b6><ad><bf>T~Uv<e5>˶{^<cb><f2>p<e5><c7>A?)7<ca>U<b1>ok<bf>V~<a3>\WyP<de><f7><8e>f<a2>#G<dd><f6>FAo8<e4><e3>쾖o<b7>k
&AzWx<a4><e1>...' to a wide string
Warning in grep("^####", full) : input string 3 is invalid
Warning in grep("^####", full) :
  unable to translate 'A<fe><ae>-<f9><8c><eb>~d<fa>"f6BI2x<c2>7Z<9c><92>2<c6>2<c5>TɅR<f8><ad><98><c0><a9>ӧ<e2><b5>쨑o<ea>\<a4><a5>5N/<ab><95><94>N<e3><9d>Ƒ<a6><a4><b6>ڠ<8b>Vpx<a0><84>4F3<e1><b4><d1>q<8f><98><8c><97><a2><b4>Zs<c6>;NQM&I*-<ac>j!<a5><eb>^<92><8...' to a wide string
Warning in grep("^####", full) : input string 4 is invalid
Warning in grep("^####", full) :
  unable to translate '<bd><8f><82>ަ`<e1><ac><9c>'<86><bb>@A<a2><94>' to a wide string
Warning in grep("^####", full) : input string 5 is invalid
Warning in grep("^####", full) :
  unable to translate 'X\MA
<8b><d0>*_<e7><84><e6><c6><d5>b<bb>h<97><86><f1><b0><83>'<d2><e1><e0>1wq<d4><e1><b8>۳pA<c8><e8><f5>f<a4>t<92><d6>9I<cf><c1>px<8c><c6>k' to a wide string
Warning in grep("^####", full) :
  unable to translate '<e7><c5>Wću<91><86>s&<c6>*$<8a>H(<81>h<c1>xg<ae>^W,]lK{ȸm2<b5>…0<ea>e*/<87><87>du\mw(h<89>h<87>Æaˀ<c1><bd><96><af><b0><fd><86>p<d4><c1><ff>4<e9>'ֶ
<a2>tl<ed><de>' to a wide string
Warning in grep("^####", full) :
  unable to translate '<d2>u<e1>H"<ce>u<8d><84>`<e1><82>.<a8>0;\<fa>h<8a><f2>' to a wide string
Warning in grep("^####", full) :
  unable to translate 'N}<89>Ċ6	<83><fc>C<b0><a2><ca><d8><ed><fc>r?&<9a>!<f2><89>Ј<9e><c9><9c>#<86>9<ad>0<fd>W<c4>7<92>#<b3>pD G<9a>sD' to a wide string
Warning in grep("^####", full) :
  unable to translate '<b3><84>Rp' to a wide string
Warning in grep("^####", full) :
  unable to translate '6a<a2>' to a wide string
Warning in grep("^####", full) :
  unable to translate 'KL<b4>B<d3><f3>L<ad>\<c4>H<9b>:_8' to a wide string
Warning in grep("^####", full) :
  unable to translate '><ea><e9><93><88>o1	<84><8d><be>̖'<80><bc>T4<ec><b3>G+28E⯀@<e4><b0>D<a3>Pt<9b>!kM夕<82><a3>F̭<b2>*\0<9c><b4>T<af>w!(Ӂ`<9b><b6><92><d2><e9>@p<cf>E<82><ac><cf>]<cb><ca>4<b8><a8>!<98><82>ف`<8d><8d><e1>e<83>Ed<b0> P:' 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
* 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
  ‘/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 4.4.1 (2024-06-14) -- "Race for Your Life"
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 0 | WARN 0 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
  3.032   0.548  13.310