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This page was generated on 2025-03-19 11:48 -0400 (Wed, 19 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4742
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4459
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 1332/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MotifPeeker 0.99.13  (landing page)
Hiranyamaya Dash
Snapshot Date: 2025-03-18 13:40 -0400 (Tue, 18 Mar 2025)
git_url: https://git.bioconductor.org/packages/MotifPeeker
git_branch: devel
git_last_commit: 665ef16
git_last_commit_date: 2025-01-06 06:01:59 -0400 (Mon, 06 Jan 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64... NOT SUPPORTED ...
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.7.1 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 kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: MotifPeeker
Version: 0.99.13
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:MotifPeeker.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MotifPeeker_0.99.13.tar.gz
StartedAt: 2025-03-19 08:49:57 -0000 (Wed, 19 Mar 2025)
EndedAt: 2025-03-19 08:56:36 -0000 (Wed, 19 Mar 2025)
EllapsedTime: 398.3 seconds
RetCode: 0
Status:   OK  
CheckDir: MotifPeeker.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:MotifPeeker.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MotifPeeker_0.99.13.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/MotifPeeker.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MotifPeeker/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MotifPeeker’ version ‘0.99.13’
* 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 loading without being on the library search path ... 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_JASPAR 0.536  0.072   5.687
* 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
  ‘/home/biocbuild/bbs-3.21-bioc/meat/MotifPeeker.Rcheck/00check.log’
for details.


Installation output

MotifPeeker.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL MotifPeeker
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘MotifPeeker’ ...
** this is package ‘MotifPeeker’ version ‘0.99.13’
** 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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 
 25.143   2.423  27.389 

Example timings

MotifPeeker.Rcheck/MotifPeeker-Ex.timings

nameusersystemelapsed
MotifPeeker0.7510.0040.757
bpapply4.3420.1004.453
calc_frip0.5450.4280.767
check_ENCODE0.6850.1043.378
check_JASPAR0.5360.0725.687
check_genome_build0.0300.0190.049
denovo_motifs0.0620.0520.117
find_motifs0.0790.0120.091
format_exptype000
get_JASPARCORE0.5320.0992.099
get_df_distances0.0660.0160.082
get_df_enrichment0.0780.0120.089
motif_enrichment0.0800.0040.084
motif_similarity0.1270.1600.287
pipe000
pretty_number0.0000.0010.000
read_motif_file0.0000.0120.013
read_peak_file0.1690.0900.260
read_peak_file_macs0.2190.0760.295
report_command0.0000.0010.001
report_header0.0000.0040.004
save_peak_file0.0480.0410.090
segregate_seqs0.1570.0520.210
summit_to_motif0.0860.0160.102
to_plotly0.2900.1000.391
trim_seqs0.0310.0080.040