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This page was generated on 2024-07-12 17:42 -0400 (Fri, 12 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4741
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4483
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4512
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4461
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1199/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
memes 1.12.0  (landing page)
Spencer Nystrom
Snapshot Date: 2024-07-10 14:00 -0400 (Wed, 10 Jul 2024)
git_url: https://git.bioconductor.org/packages/memes
git_branch: RELEASE_3_19
git_last_commit: 658eb6b
git_last_commit_date: 2024-04-30 11:32:21 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for memes on kjohnson1

To the developers/maintainers of the memes package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/memes.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: memes
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:memes.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings memes_1.12.0.tar.gz
StartedAt: 2024-07-12 00:37:41 -0400 (Fri, 12 Jul 2024)
EndedAt: 2024-07-12 00:39:54 -0400 (Fri, 12 Jul 2024)
EllapsedTime: 133.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: memes.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:memes.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings memes_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/memes.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘memes/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘memes’ version ‘1.12.0’
* 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 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
add_sequence 8.815  0.252   9.072
* 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 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/memes.Rcheck/00check.log’
for details.


Installation output

memes.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL memes
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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)

Tests output


Example timings

memes.Rcheck/memes-Ex.timings

nameusersystemelapsed
add_sequence8.8150.2529.072
ame_compare_heatmap_methods1.9580.0412.001
check_meme_install0.5010.0620.567
drop_best_match0.0070.0020.008
example_ame0.0610.0040.065
example_ame_large0.0360.0040.040
force_best_match0.0500.0060.056
get_sequence0.3980.0580.469
has_duplicate_motifs0.1980.0130.211
importAme0.2250.0320.254
importDremeXML0.1960.0060.202
importFimo0.0400.0070.043
importMeme0.1050.0030.108
importStremeXML0.1260.0040.130
importTomTomXML0.2480.0040.252
meme_is_installed0.0470.0010.048
nest_tomtom0.0470.0010.048
plot_ame_heatmap0.4890.0080.499
plot_sequence_heatmap2.7500.0742.826
remove_duplicate_motifs0.0030.0010.003
runAme0.0500.0010.050
runDreme0.0480.0010.050
runFimo0.0510.0030.054
runMeme0.0510.0040.055
runTomTom0.0510.0040.055
update_best_match0.0750.0050.079
view_tomtom_hits0.8360.0410.877
write_fasta0.0030.0010.003