Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-07 20:27 -0400 (Fri, 07 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4755 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4489 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4520 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
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 1199/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
memes 1.12.0 (landing page) Spencer Nystrom
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
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. |
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: 2024-06-05 21:24:55 -0400 (Wed, 05 Jun 2024) |
EndedAt: 2024-06-05 21:27:15 -0400 (Wed, 05 Jun 2024) |
EllapsedTime: 140.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: memes.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### 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 4.4.0 (2024-04-24) * using platform: x86_64-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 Monterey 12.7.1 * 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 8.182 0.298 8.512 * 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.
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-x86_64/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)
memes.Rcheck/memes-Ex.timings
name | user | system | elapsed | |
add_sequence | 8.182 | 0.298 | 8.512 | |
ame_compare_heatmap_methods | 1.949 | 0.054 | 2.009 | |
check_meme_install | 0.477 | 0.060 | 0.539 | |
drop_best_match | 0.006 | 0.003 | 0.008 | |
example_ame | 0.071 | 0.007 | 0.078 | |
example_ame_large | 0.046 | 0.004 | 0.050 | |
force_best_match | 0.060 | 0.007 | 0.068 | |
get_sequence | 0.513 | 0.070 | 0.588 | |
has_duplicate_motifs | 0.213 | 0.010 | 0.225 | |
importAme | 0.265 | 0.050 | 0.306 | |
importDremeXML | 0.242 | 0.007 | 0.251 | |
importFimo | 0.052 | 0.012 | 0.055 | |
importMeme | 0.108 | 0.003 | 0.112 | |
importStremeXML | 0.175 | 0.004 | 0.180 | |
importTomTomXML | 0.341 | 0.004 | 0.347 | |
meme_is_installed | 0.063 | 0.001 | 0.064 | |
nest_tomtom | 0.045 | 0.000 | 0.046 | |
plot_ame_heatmap | 0.548 | 0.009 | 0.558 | |
plot_sequence_heatmap | 3.183 | 0.102 | 3.325 | |
remove_duplicate_motifs | 0.002 | 0.001 | 0.004 | |
runAme | 0.061 | 0.002 | 0.062 | |
runDreme | 0.047 | 0.001 | 0.048 | |
runFimo | 0.044 | 0.003 | 0.046 | |
runMeme | 0.055 | 0.001 | 0.057 | |
runTomTom | 0.051 | 0.001 | 0.052 | |
update_best_match | 0.096 | 0.004 | 0.100 | |
view_tomtom_hits | 1.022 | 0.027 | 1.053 | |
write_fasta | 0.003 | 0.001 | 0.003 | |