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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:memes.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings memes_1.17.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/memes.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 ‘memes/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘memes’ version ‘1.17.2’
* 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 ‘memes’ 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 ... WARNING
motif_input:
  function(x, ...)
motif_input.universalmotif_df:
  function(input, path)

motif_input:
  function(x, ...)
motif_input.universalmotif:
  function(input, path)

motif_input:
  function(x, ...)
motif_input.list:
  function(input, path)

motif_input:
  function(x, ...)
motif_input.character:
  function(input, path)

motif_input:
  function(x, ...)
motif_input.data.frame:
  function(input, path)

sequence_input:
  function(x)
sequence_input.DNAStringSet:
  function(input)

sequence_input:
  function(x)
sequence_input.character:
  function(input)

sequence_input:
  function(x)
sequence_input.BStringSet:
  function(input)

sequence_input:
  function(x)
sequence_input.AAStringSet:
  function(input)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) runTomTom.Rd:51: Lost braces; missing escapes or markup?
    51 | \item{...}{additional flags passed to tomtom using {cmdfun} formating (see table below for details)}
       |                                                    ^
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘memes-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: runDreme
> ### Title: Denovo motif discovery of target regions using DREME
> ### Aliases: runDreme
> 
> ### ** Examples
> 
> if (meme_is_installed()) {
+ # Create random named sequences as input for example
+ seqs <- universalmotif::create_sequences(rng.seed = 123)
+ names(seqs) <- seq_along(seqs)
+ 
+ # Runs dreme with default settings, shuffles input as background
+ runDreme(seqs, "shuffle")
+ 
+ # Runs searching for max 2 motifs, e-value cutoff = 0.1, explicitly using the DNA alphabet
+ runDreme(seqs, "shuffle", nmotifs = 2, e = 0.1, dna = TRUE)
+ }
Error in `process_initialize(self, private, command, args, stdin, stdout, …`:
! Native call to `processx_exec` failed
Caused by error in `chain_call(c_processx_exec, command, c(command, args), pty, pty_options, …`:
! cannot start processx process '/opt/meme/bin/dreme' (system error 2, No such file or directory) @unix/processx.c:611 (processx_exec)
---
Backtrace:
 1. memes::runDreme(seqs, "shuffle")
 2. memes:::runDreme.default(seqs, "shuffle")
 3. processx::run(command, flags, spinner = TRUE, error_on_status = FALSE)
 4. process$new(command, args, echo_cmd = echo_cmd, wd = wd, windows_verbatim_…
 5. local initialize(...)
 6. processx:::process_initialize(self, private, command, args, stdin, stdout, …
 7. processx:::chain_call(c_processx_exec, command, c(command, args), pty, pty_options, …
 8. | base::withCallingHandlers(do.call(".Call", list(.NAME, ...)), error = function(e…
 9. | base::do.call(".Call", list(.NAME, ...))
10. | base::.handleSimpleError(function (e) …
11. | local h(simpleError(msg, call))
12. | processx:::throw_error(err, parent = e)
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
runAme                10.928  0.710   9.915
add_sequence           8.869  0.379   9.274
plot_sequence_heatmap  6.722  0.399   7.145
* 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, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/memes.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL memes
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘memes’ ...
** this is package ‘memes’ version ‘1.17.2’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (memes)