Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-31 17:03:04 -0400 (Fri, 31 May 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" | 4753 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
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 | |||||||||
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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:memes.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings memes_1.12.0.tar.gz |
StartedAt: 2024-05-31 05:17:45 -0400 (Fri, 31 May 2024) |
EndedAt: 2024-05-31 05:20:49 -0400 (Fri, 31 May 2024) |
EllapsedTime: 183.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: memes.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:memes.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings memes_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/memes.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * 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 ‘1.12.0’ * 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 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 7.465 0.389 7.854 * 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 ‘/home/biocbuild/bbs-3.19-bioc/meat/memes.Rcheck/00check.log’ for details.
memes.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL memes ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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)
memes.Rcheck/memes-Ex.timings
name | user | system | elapsed | |
add_sequence | 7.465 | 0.389 | 7.854 | |
ame_compare_heatmap_methods | 1.613 | 0.124 | 1.736 | |
check_meme_install | 0.438 | 0.099 | 0.538 | |
drop_best_match | 0.003 | 0.004 | 0.006 | |
example_ame | 0.057 | 0.000 | 0.058 | |
example_ame_large | 0.036 | 0.000 | 0.036 | |
force_best_match | 0.044 | 0.000 | 0.044 | |
get_sequence | 0.347 | 0.012 | 0.358 | |
has_duplicate_motifs | 0.170 | 0.027 | 0.198 | |
importAme | 0.198 | 0.069 | 0.269 | |
importDremeXML | 0.185 | 0.003 | 0.189 | |
importFimo | 0.040 | 0.012 | 0.047 | |
importMeme | 0.128 | 0.000 | 0.129 | |
importStremeXML | 0.123 | 0.004 | 0.127 | |
importTomTomXML | 0.255 | 0.000 | 0.256 | |
meme_is_installed | 0.047 | 0.000 | 0.047 | |
nest_tomtom | 0.042 | 0.003 | 0.045 | |
plot_ame_heatmap | 0.480 | 0.008 | 0.489 | |
plot_sequence_heatmap | 2.790 | 0.227 | 3.018 | |
remove_duplicate_motifs | 0.003 | 0.001 | 0.003 | |
runAme | 0.05 | 0.00 | 0.05 | |
runDreme | 0.043 | 0.004 | 0.047 | |
runFimo | 0.053 | 0.000 | 0.053 | |
runMeme | 0.051 | 0.000 | 0.051 | |
runTomTom | 0.047 | 0.000 | 0.047 | |
update_best_match | 0.067 | 0.004 | 0.071 | |
view_tomtom_hits | 0.816 | 0.036 | 0.853 | |
write_fasta | 0.003 | 0.000 | 0.003 | |