Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-10-09 11:41 -0400 (Thu, 09 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4832
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4613
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4554
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4585
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 557/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEP 1.30.0  (landing page)
Arne Smits
Snapshot Date: 2025-10-06 13:40 -0400 (Mon, 06 Oct 2025)
git_url: https://git.bioconductor.org/packages/DEP
git_branch: RELEASE_3_21
git_last_commit: 0ba4621
git_last_commit_date: 2025-04-15 11:13:15 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  


CHECK results for DEP on kunpeng2

To the developers/maintainers of the DEP package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DEP.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: DEP
Version: 1.30.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:DEP.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DEP_1.30.0.tar.gz
StartedAt: 2025-10-07 08:37:58 -0000 (Tue, 07 Oct 2025)
EndedAt: 2025-10-07 08:47:02 -0000 (Tue, 07 Oct 2025)
EllapsedTime: 544.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: DEP.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:DEP.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DEP_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/DEP.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 ‘DEP/DESCRIPTION’ ... OK
* this is package ‘DEP’ version ‘1.30.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 23 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 ‘DEP’ 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 whether startup messages can be suppressed ... 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 ... WARNING
Missing link(s) in Rd file 'LFQ.Rd':
  ‘[MSnbase:impute-methods]{impute}’

Missing link(s) in Rd file 'TMT.Rd':
  ‘[MSnbase:impute-methods]{impute}’

Missing link(s) in Rd file 'impute.Rd':
  ‘[MSnbase:impute-methods]{impute}’

Missing link(s) in Rd file 'process.Rd':
  ‘[MSnbase:impute-methods]{impute}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
impute       34.287  0.283  34.671
plot_volcano  5.314  0.088   5.425
plot_dist     5.324  0.024   5.367
* 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 WARNING
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/DEP.Rcheck/00check.log’
for details.


Installation output

DEP.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘DEP’ ...
** this is package ‘DEP’ version ‘1.30.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (DEP)

Tests output

DEP.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.

> library(testthat)
> library(DEP)
> 
> test_check("DEP")
[ FAIL 0 | WARN 15 | SKIP 0 | PASS 333 ]

[ FAIL 0 | WARN 15 | SKIP 0 | PASS 333 ]
> 
> proc.time()
   user  system elapsed 
 71.935   2.629  74.884 

Example timings

DEP.Rcheck/DEP-Ex.timings

nameusersystemelapsed
LFQ2.8170.0322.857
TMT000
add_rejections1.0110.0631.079
analyze_dep2.960.022.99
filter_missval1.7730.0281.806
filter_proteins0.380.040.42
get_df_long1.0610.0481.113
get_df_wide1.0460.0041.053
get_prefix0.0030.0000.003
get_results1.3920.0121.409
get_suffix0.0000.0010.001
import_IsobarQuant000
import_MaxQuant0.0670.0010.068
impute34.287 0.28334.671
make_se0.0540.0040.058
make_se_parse0.0910.0120.103
make_unique0.0240.0000.024
manual_impute0.9100.0160.929
meanSdPlot0.7670.0440.814
normalize_vsn0.4780.0360.516
plot_all2.4930.0352.541
plot_cond1.4970.0041.507
plot_cond_freq2.3900.0322.430
plot_cond_overlap1.2790.0081.292
plot_cor1.7760.0121.795
plot_coverage0.7070.0040.713
plot_detect1.0200.0001.024
plot_dist5.3240.0245.367
plot_frequency0.5740.0240.600
plot_gsea0.9600.0160.980
plot_heatmap3.6560.0203.689
plot_imputation1.4100.0121.427
plot_missval2.2340.0482.289
plot_normalization1.9070.0441.957
plot_numbers0.6450.0110.660
plot_p_hist1.7340.0081.748
plot_pca1.7070.0001.712
plot_single2.2120.0122.232
plot_volcano5.3140.0885.425
process1.9860.0282.021
report0.0000.0000.001
run_app000
se2msn0.1620.0030.166
test_diff1.2510.0081.263
test_gsea0.9980.0001.002
theme_DEP10.6050.0000.607
theme_DEP20.7030.0000.706