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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:memes.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings memes_1.13.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/memes.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.5 LTS
* using session charset: UTF-8
* checking for file ‘memes/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘memes’ version ‘1.13.0’
* 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 ‘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: force_best_match
> ### Title: Force best tomtom match by id
> ### Aliases: force_best_match
> 
> ### ** Examples
> 
> if (meme_is_installed()){
+ motif <- universalmotif::create_motif("CCRAAAW", name = "example_motif")
+ db <- system.file("extdata", "flyFactorSurvey_cleaned.meme", package = "memes")
+ res <- runTomTom(motif, database = db)
+ res$best_match_name
+ res2 <- force_best_match(res, c("example_motif" = "Eip93F_SANGER_10"))
+ res2$best_match_name
+ }
Warning: tomtom_xml_to_html exited abnormally and may have failed to create HTML output.
Writing results to output directory '/tmp/Rtmpdb5nwy/tomtom'.
Processing query 1 out of 1 
# Computing q-values.
#   Estimating pi_0 from all 1112 observed p-values.
#   Estimating pi_0.
# Minimal pi_zero = 1.00322
#   Estimated pi_0=1
Can't locate XML/Parser/Expat.pm in @INC (you may need to install the XML::Parser::Expat module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.34.0 /usr/local/share/perl/5.34.0 /usr/lib/x86_64-linux-gnu/perl5/5.34 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl-base /usr/lib/x86_64-linux-gnu/perl/5.34 /usr/share/perl/5.34 /usr/local/lib/site_perl) at /opt/meme/libexec/meme-5.5.5/tomtom_xml_to_html line 21.
BEGIN failed--compilation aborted at /opt/meme/libexec/meme-5.5.5/tomtom_xml_to_html line 21.
Warning: tomtom_xml_to_html exited abnormally and may have failed to create HTML output.

Error: Shell process had non-zero exit status.
Execution halted
* 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, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/memes.Rcheck/00check.log’
for details.

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