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This page was generated on 2025-08-14 11:44 -0400 (Thu, 14 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4566
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R 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 1347/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MotifPeeker 1.0.0  (landing page)
Hiranyamaya Dash
Snapshot Date: 2025-08-11 13:40 -0400 (Mon, 11 Aug 2025)
git_url: https://git.bioconductor.org/packages/MotifPeeker
git_branch: RELEASE_3_21
git_last_commit: defac3c
git_last_commit_date: 2025-04-15 13:44:12 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64... NOT SUPPORTED ...
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for MotifPeeker on merida1

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.

raw results


Summary

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

Command output

##############################################################################
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###
### 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.


Installation output

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)

Tests output

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 

Example timings

MotifPeeker.Rcheck/MotifPeeker-Ex.timings

nameusersystemelapsed
MotifPeeker1.4890.2971.868
bpapply4.0660.1884.192
calc_frip0.9100.4721.361
check_ENCODE 0.728 0.13310.658
check_JASPAR0.4830.0760.561
check_genome_build0.0520.0170.069
denovo_motifs0.1290.0170.147
find_motifs0.1350.0200.155
format_exptype0.0000.0000.001
get_JASPARCORE0.4990.0680.569
get_df_distances0.1330.0160.149
get_df_enrichment0.1290.0150.145
motif_enrichment0.1290.0150.144
motif_similarity0.1290.0150.146
pipe000
pretty_number0.0010.0010.001
read_motif_file0.0120.0060.019
read_peak_file0.3080.0420.350
read_peak_file_macs0.3690.0500.429
report_command0.0010.0010.001
report_header0.0040.0020.006
save_peak_file0.1020.0150.117
segregate_seqs0.2960.0440.349
summit_to_motif0.1240.0100.135
to_plotly0.4010.0850.494
trim_seqs0.0430.0040.049