Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-14 11:44 -0400 (Thu, 14 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4566 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4604 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4545 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
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 1347/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MotifPeeker 1.0.0 (landing page) Hiranyamaya Dash
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the MotifPeeker package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MotifPeeker.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: MotifPeeker |
Version: 1.0.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MotifPeeker.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MotifPeeker_1.0.0.tar.gz |
StartedAt: 2025-08-12 06:33:39 -0400 (Tue, 12 Aug 2025) |
EndedAt: 2025-08-12 06:43:19 -0400 (Tue, 12 Aug 2025) |
EllapsedTime: 580.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MotifPeeker.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MotifPeeker.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MotifPeeker_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/MotifPeeker.Rcheck’ * using R version 4.5.1 RC (2025-06-05 r88288) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MotifPeeker/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MotifPeeker’ version ‘1.0.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 25 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘MotifPeeker’ 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 ... OK * 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 ... NOTE Non-topic package-anchored link(s) in Rd file 'pipe.Rd': ‘[magrittr:pipe]{%>%}’ See section 'Cross-references' in the 'Writing R Extensions' manual. Found the following Rd file(s) with Rd \link{} targets missing package anchors: motif_enrichment.Rd: memes plot_motif_comparison.Rd: compare_motifs Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 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 check_ENCODE 0.728 0.133 10.658 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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 NOTE See ‘/Users/biocbuild/bbs-3.21-bioc/meat/MotifPeeker.Rcheck/00check.log’ for details.
MotifPeeker.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MotifPeeker ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘MotifPeeker’ ... ** this is package ‘MotifPeeker’ version ‘1.0.0’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (MotifPeeker)
MotifPeeker.Rcheck/tests/testthat.Rout
R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > desc_path <- list.files("../","^DESCRIPTION$", + full.names = TRUE, recursive = TRUE)[1] > pkg <- read.dcf(desc_path, fields = "Package")[1] > library(testthat) > library(pkg, character.only = TRUE) > > test_check(pkg) ### Exp2 {- .unlisted} **Reference Experiment Label**: Exp1 (Total Reads: 100) **Comparison Experiment Label**: Exp2 (Total Reads: 200) ## Exp2 {- .unlisted .tabset .tabset-fade .tabset-pills} **Reference Experiment Label**: Exp1 **Comparison Experiment Label**: Exp2 [ FAIL 0 | WARN 0 | SKIP 10 | PASS 63 ] ══ Skipped tests (10) ══════════════════════════════════════════════════════════ • MEME is not installed (8): 'test-MotifPeeker.R:1:1', 'test-confirm_meme_install.R:1:1', 'test-denovo_motif_funcs.R:1:1', 'test-enrichment_funcs.R:1:1', 'test-get_df_distances.R:1:1', 'test-markov_background_model.R:1:1', 'test-motif_enrichment.R:1:1', 'test-summit_to_motif.R:1:1' • On CRAN (2): 'test-check_ENCODE.R:1:1', 'test-check_JASPAR.R:1:1' [ FAIL 0 | WARN 0 | SKIP 10 | PASS 63 ] > > proc.time() user system elapsed 35.211 3.051 39.253
MotifPeeker.Rcheck/MotifPeeker-Ex.timings
name | user | system | elapsed | |
MotifPeeker | 1.489 | 0.297 | 1.868 | |
bpapply | 4.066 | 0.188 | 4.192 | |
calc_frip | 0.910 | 0.472 | 1.361 | |
check_ENCODE | 0.728 | 0.133 | 10.658 | |
check_JASPAR | 0.483 | 0.076 | 0.561 | |
check_genome_build | 0.052 | 0.017 | 0.069 | |
denovo_motifs | 0.129 | 0.017 | 0.147 | |
find_motifs | 0.135 | 0.020 | 0.155 | |
format_exptype | 0.000 | 0.000 | 0.001 | |
get_JASPARCORE | 0.499 | 0.068 | 0.569 | |
get_df_distances | 0.133 | 0.016 | 0.149 | |
get_df_enrichment | 0.129 | 0.015 | 0.145 | |
motif_enrichment | 0.129 | 0.015 | 0.144 | |
motif_similarity | 0.129 | 0.015 | 0.146 | |
pipe | 0 | 0 | 0 | |
pretty_number | 0.001 | 0.001 | 0.001 | |
read_motif_file | 0.012 | 0.006 | 0.019 | |
read_peak_file | 0.308 | 0.042 | 0.350 | |
read_peak_file_macs | 0.369 | 0.050 | 0.429 | |
report_command | 0.001 | 0.001 | 0.001 | |
report_header | 0.004 | 0.002 | 0.006 | |
save_peak_file | 0.102 | 0.015 | 0.117 | |
segregate_seqs | 0.296 | 0.044 | 0.349 | |
summit_to_motif | 0.124 | 0.010 | 0.135 | |
to_plotly | 0.401 | 0.085 | 0.494 | |
trim_seqs | 0.043 | 0.004 | 0.049 | |