Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-10-13 11:41 -0400 (Mon, 13 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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: 2025-10-09 13:40 -0400 (Thu, 09 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: 2025-10-10 08:09:15 -0000 (Fri, 10 Oct 2025)
EndedAt: 2025-10-10 08:18:57 -0000 (Fri, 10 Oct 2025)
EllapsedTime: 582.3 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       35.400  0.287  35.759
plot_volcano  6.208  0.059   6.282
plot_dist     5.364  0.008   5.385
* 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 16 | SKIP 0 | PASS 333 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 333 ]
> 
> proc.time()
   user  system elapsed 
 81.970   2.898  85.148 

Example timings

DEP.Rcheck/DEP-Ex.timings

nameusersystemelapsed
LFQ1.8720.0001.877
TMT000
add_rejections2.0350.0162.054
analyze_dep3.2400.0563.304
filter_missval0.6840.0040.689
filter_proteins0.4170.0040.422
get_df_long1.0890.0001.092
get_df_wide1.0430.0081.054
get_prefix0.0020.0000.003
get_results1.4470.0121.462
get_suffix0.0020.0000.001
import_IsobarQuant0.0010.0000.000
import_MaxQuant0.0700.0000.071
impute35.400 0.28735.759
make_se0.0520.0040.055
make_se_parse0.0790.0040.083
make_unique0.0240.0000.024
manual_impute0.9120.0200.934
meanSdPlot0.9290.0520.983
normalize_vsn0.4700.0000.469
plot_all2.7600.0162.782
plot_cond1.6380.0081.649
plot_cond_freq1.3550.0001.358
plot_cond_overlap1.4120.0001.415
plot_cor1.7370.0001.741
plot_coverage0.8730.0000.875
plot_detect1.4300.0321.465
plot_dist5.3640.0085.385
plot_frequency0.7380.0000.739
plot_gsea0.9850.0000.988
plot_heatmap3.7010.0483.759
plot_imputation1.6670.0001.671
plot_missval2.2900.0242.320
plot_normalization2.4110.0322.449
plot_numbers0.8610.0000.862
plot_p_hist2.1620.0282.195
plot_pca2.1450.0122.162
plot_single3.1260.0003.133
plot_volcano6.2080.0596.282
process2.3940.0072.408
report0.0010.0000.000
run_app000
se2msn0.1860.0030.190
test_diff1.2630.0081.273
test_gsea1.0330.0001.036
theme_DEP10.7590.0000.759
theme_DEP20.8770.0000.879