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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:STADyUM.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings STADyUM_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/STADyUM.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘STADyUM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘STADyUM’ version ‘1.0.0’
* 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 ‘STADyUM’ can be installed ... OK
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  TranscriptionRates-class.Rd: ggplot2
  TranscriptionRatesLRT-class.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                     user system elapsed
SimulationTranscriptionRates-class 49.951  3.274  61.546
ExperimentTranscriptionRates-class 48.371  0.505  63.010
rates                              47.568  0.142  53.803
stericHindrance                    47.228  0.221  48.068
estimateTranscriptionRates         46.507  0.076  53.462
TranscriptionRatesLRT-class        16.523  0.168  19.724
SimulatePolymerase-class           10.065  0.213  12.279
TranscriptionRates-class            4.758  0.216   5.697
* 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:
      fk <- dnorm(kmin:kmax, mean = fkMean, sd = fkVar^0.5)
      fk <- fk/sum(fk)
  }`: missing value where TRUE/FALSE needed
  Backtrace:
      ▆
   1. ├─STADyUM::estimateTranscriptionRates(simpol2, name = "high_k_high_beta") at test_sim_lrts.R:13:5
   2. └─STADyUM::estimateTranscriptionRates(simpol2, name = "high_k_high_beta")
   3.   └─STADyUM (local) .local(x, ...)
   4.     └─STADyUM:::runEmAlgorithm(bwDfs, params, stericHindrance)
   5.       └─STADyUM:::pauseEscapeEM(...)
   6.         └─STADyUM:::pauseEscapeMaximization(...)
  
  [ FAIL 1 | WARN 38 | SKIP 0 | PASS 14 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/STADyUM.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL STADyUM
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘STADyUM’ ...
** this is package ‘STADyUM’ version ‘1.0.0’
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c simPol.cpp -o simPol.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o STADyUM.so RcppExports.o simPol.o -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/site-library/00LOCK-STADyUM/00new/STADyUM/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (STADyUM)

R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(STADyUM)
> 
> test_check("STADyUM")

Importing bigwig files...

Processing plus and minus strands bigwig...

Summarizing pause and gene body regions...

Generating read counts table...
estimating rates...

Importing bigwig files...

Processing plus and minus strands bigwig...

Summarizing pause and gene body regions...

Generating read counts table...
estimating rates...
Total time used for the simulation is 0.0166667 mins.
Total time used for the simulation is 0 mins.
Starting EM algorithm...
Starting EM algorithm...
[ FAIL 1 | WARN 38 | SKIP 0 | PASS 14 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_sim_lrts.R:13:5'): Simulated Transcription Rates Likelihood Ratio Test works as intented ──
Error in `if (fkVar < 1e-10) {
    fk[seq_len(length(fk))] <- 0
    fk[round(fkMean)] <- 1
} else {
    fk <- dnorm(kmin:kmax, mean = fkMean, sd = fkVar^0.5)
    fk <- fk/sum(fk)
}`: missing value where TRUE/FALSE needed
Backtrace:
    ▆
 1. ├─STADyUM::estimateTranscriptionRates(simpol2, name = "high_k_high_beta") at test_sim_lrts.R:13:5
 2. └─STADyUM::estimateTranscriptionRates(simpol2, name = "high_k_high_beta")
 3.   └─STADyUM (local) .local(x, ...)
 4.     └─STADyUM:::runEmAlgorithm(bwDfs, params, stericHindrance)
 5.       └─STADyUM:::pauseEscapeEM(...)
 6.         └─STADyUM:::pauseEscapeMaximization(...)

[ FAIL 1 | WARN 38 | SKIP 0 | PASS 14 ]
Error: Test failures
Execution halted