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This page was generated on 2023-10-20 09:38:05 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 1157/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
memes 1.8.0  (landing page)
Spencer Nystrom
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/memes
git_branch: RELEASE_3_17
git_last_commit: d19360d
git_last_commit_date: 2023-04-25 11:27:46 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for memes on kjohnson2


To the developers/maintainers of the memes package:
- 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: 1.8.0
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_1.8.0.tar.gz
StartedAt: 2023-10-18 05:32:14 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 05:35:45 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 210.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: memes.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/memes.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘memes/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘memes’ version ‘1.8.0’
* 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 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 7.717  0.269  12.194
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/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/4.3-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_sequence 7.717 0.26912.194
ame_compare_heatmap_methods1.1450.0701.738
check_meme_install0.6010.0290.894
drop_best_match0.0090.0020.019
example_ame0.0700.0020.109
example_ame_large0.0460.0010.074
force_best_match0.0580.0010.090
get_sequence0.4320.0370.700
has_duplicate_motifs0.9390.0181.475
importAme0.2540.0350.486
importDremeXML0.2780.0090.436
importFimo0.0540.0050.104
importMeme0.1400.0050.198
importStremeXML0.2260.0070.349
importTomTomXML0.4760.0370.796
meme_is_installed0.0680.0070.116
nest_tomtom0.0800.0090.138
plot_ame_heatmap0.5390.0380.890
plot_sequence_heatmap3.1320.1044.546
remove_duplicate_motifs0.0030.0010.003
runAme0.0600.0020.068
runDreme0.0600.0020.069
runFimo0.0610.0020.069
runMeme0.0610.0020.075
runTomTom0.0610.0020.083
update_best_match0.1180.0050.181
view_tomtom_hits1.1390.0221.639
write_fasta0.0030.0000.008