Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-09-23 12:04 -0400 (Tue, 23 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4816
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4605
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4549
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4560
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 558/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEP 1.31.2  (landing page)
Arne Smits
Snapshot Date: 2025-09-22 13:45 -0400 (Mon, 22 Sep 2025)
git_url: https://git.bioconductor.org/packages/DEP
git_branch: devel
git_last_commit: 96d07f1
git_last_commit_date: 2025-08-22 08:28:23 -0400 (Fri, 22 Aug 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for DEP on lconway

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.

raw results


Summary

Package: DEP
Version: 1.31.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DEP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DEP_1.31.2.tar.gz
StartedAt: 2025-09-22 20:33:24 -0400 (Mon, 22 Sep 2025)
EndedAt: 2025-09-22 20:42:05 -0400 (Mon, 22 Sep 2025)
EllapsedTime: 520.7 seconds
RetCode: 0
Status:   OK  
CheckDir: DEP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DEP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DEP_1.31.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/DEP.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 ‘DEP/DESCRIPTION’ ... OK
* this is package ‘DEP’ version ‘1.31.2’
* 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 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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'LFQ.Rd':
  ‘[MSnbase:impute]{impute}’

Non-topic package-anchored link(s) in Rd file 'TMT.Rd':
  ‘[MSnbase:impute]{impute}’

Non-topic package-anchored link(s) in Rd file 'impute.Rd':
  ‘[MSnbase:impute]{impute}’

Non-topic package-anchored link(s) in Rd file 'process.Rd':
  ‘[MSnbase:impute]{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       49.942  0.334  50.483
plot_volcano  5.160  0.049   5.239
* 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-3.22-bioc/meat/DEP.Rcheck/00check.log’
for details.


Installation output

DEP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DEP
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘DEP’ ...
** this is package ‘DEP’ version ‘1.31.2’
** 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
Warning in fun(libname, pkgname) :
  Package 'DEP' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'DEP' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (DEP)

Tests output

DEP.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "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.

> library(testthat)
> library(DEP)
Warning message:
In fun(libname, pkgname) :
  Package 'DEP' is deprecated and will be removed from Bioconductor
  version 3.23
> 
> test_check("DEP")
[ FAIL 0 | WARN 15 | SKIP 0 | PASS 333 ]

[ FAIL 0 | WARN 15 | SKIP 0 | PASS 333 ]
> 
> proc.time()
   user  system elapsed 
 68.323   3.388  73.245 

Example timings

DEP.Rcheck/DEP-Ex.timings

nameusersystemelapsed
LFQ1.4900.0381.549
TMT0.0000.0000.001
add_rejections1.6520.0171.682
analyze_dep2.4870.0892.590
filter_missval0.4760.0060.484
filter_proteins0.3010.0110.316
get_df_long0.8100.0130.825
get_df_wide0.8200.0170.842
get_prefix0.0030.0010.003
get_results1.9420.0261.974
get_suffix0.0010.0000.001
import_IsobarQuant000
import_MaxQuant0.0550.0010.057
impute49.942 0.33450.483
make_se0.0490.0000.049
make_se_parse0.0710.0010.072
make_unique0.0190.0010.019
manual_impute1.5700.0351.610
meanSdPlot0.9740.0341.024
normalize_vsn0.3280.0020.332
plot_all1.9080.0311.947
plot_cond1.2210.0191.247
plot_cond_freq1.0470.0131.063
plot_cond_overlap1.0470.0141.063
plot_cor1.3140.0251.344
plot_coverage0.5630.0030.568
plot_detect0.9840.0080.995
plot_dist4.0430.0364.101
plot_frequency0.5600.0050.570
plot_gsea0.6920.0060.700
plot_heatmap2.6090.0302.648
plot_imputation1.2720.0271.311
plot_missval1.6340.0501.690
plot_normalization1.6550.0361.699
plot_numbers0.5930.0060.602
plot_p_hist1.7510.0551.814
plot_pca1.6950.0201.724
plot_single2.5080.0202.536
plot_volcano5.1600.0495.239
process1.7910.0301.829
report0.0000.0000.001
run_app000
se2msn0.1300.0010.132
test_diff0.9690.0100.981
test_gsea0.7860.0130.801
theme_DEP10.5970.0070.606
theme_DEP20.6840.0080.693