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### Running command:
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###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:memes.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings memes_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/memes.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* 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 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘memes/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘memes’ 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 ... 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 R 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 ... 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 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
add_sequence 7.312  0.348    7.66
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘core_ame.Rmd’ using ‘UTF-8’... failed
  ‘core_dreme.Rmd’ using ‘UTF-8’... failed
  ‘core_fimo.Rmd’ using ‘UTF-8’... failed
  ‘core_tomtom.Rmd’ using ‘UTF-8’... OK
  ‘install_guide.Rmd’ using ‘UTF-8’... OK
  ‘integrative_analysis.Rmd’ using ‘UTF-8’... failed
  ‘tidy_motifs.Rmd’ using ‘UTF-8’... OK
 ERROR
Errors in running code in vignettes:
when running code in ‘core_ame.Rmd’
  ...

> ame_by_behavior_vs_static <- runAme(seq_by_behavior, 
+     control = "Static")

  When sourcing ‘core_ame.R’:
Error: ℹ In index: 1.
ℹ With name: Decreasing.
Caused by error in `.check_valid_command_path()`:
! Command: /home/biocbuild/meme/bin, does not exist.
Execution halted
when running code in ‘core_dreme.Rmd’
  ...
Cannot detect meme install

> fa <- system.file("extdata/fasta_ex/fa1.fa", package = "memes")

> dreme_out <- runDreme(fa, "shuffle", evalue = 39, 
+     outdir = tempdir())

  When sourcing ‘core_dreme.R’:
Error: Command: /home/biocbuild/meme/bin, does not exist.
Execution halted
when running code in ‘core_fimo.Rmd’
  ...
+     universalmotif::convert_motifs() %>% .[[1]]
See system.file("LICENSE", package="MotifDb") for use restrictions.

> e93_motif["name"] <- "E93_FlyFactor"

> fimo_results <- runFimo(sequences, e93_motif)

  When sourcing ‘core_fimo.R’:
Error: Command: /home/biocbuild/meme/bin, does not exist.
Execution halted
when running code in ‘integrative_analysis.Rmd’
  ...
[["orphan"]] chr3L:57749-57848=GAAACCTATACCCCGCCGTCGGCCGATTATCACCTTTTCAAGTCTC...

> ame_by_binding <- by_binding %>% runAme

  When sourcing ‘integrative_analysis.R’:
Error: ℹ In index: 1.
ℹ With name: ectopic.
Caused by error in `.check_valid_command_path()`:
! Command: /home/biocbuild/meme/bin, does not exist.
Execution halted

* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/memes.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL memes
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* installing to library ‘/home/biocbuild/bbs-3.18-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)