Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 1190/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
memes 1.14.0  (landing page)
Spencer Nystrom
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/memes
git_branch: RELEASE_3_20
git_last_commit: 25c7604
git_last_commit_date: 2024-10-29 10:57:14 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  


CHECK results for memes on teran2

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: 1.14.0
Command: /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_1.14.0.tar.gz
StartedAt: 2024-11-20 05:23:39 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 05:26:03 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 144.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: memes.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /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_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/memes.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘memes/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘memes’ version ‘1.14.0’
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
add_sequence 5.850  0.291   6.143
runAme       5.373  0.436   4.856
* 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 WARNING, 1 NOTE
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/memes.Rcheck/00check.log’
for details.


Installation output

memes.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL memes
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/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)

Tests output


Example timings

memes.Rcheck/memes-Ex.timings

nameusersystemelapsed
add_sequence5.8500.2916.143
ame_compare_heatmap_methods1.4700.0621.532
check_meme_install0.4410.1150.557
drop_best_match0.0050.0000.004
example_ame0.0420.0060.048
example_ame_large0.0270.0050.032
force_best_match0.7520.1970.984
get_sequence0.2710.0710.347
has_duplicate_motifs0.0030.0020.008
importAme0.1270.0560.183
importDremeXML0.1210.0140.135
importFimo0.0210.0090.030
importMeme0.0600.0090.071
importStremeXML0.1290.0170.146
importTomTomXML0.1660.0140.181
meme_is_installed0.0330.0000.033
nest_tomtom0.5720.1350.703
plot_ame_heatmap0.3770.0420.420
plot_sequence_heatmap1.9780.1242.106
remove_duplicate_motifs0.0020.0000.002
runAme5.3730.4364.856
runDreme1.3250.3451.683
runFimo0.1850.1270.318
runMeme0.5580.3201.269
runTomTom0.5990.1320.728
update_best_match0.0590.0060.066
view_tomtom_hits0.6320.0940.727
write_fasta0.0000.0020.002