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This page was generated on 2025-09-02 12:04 -0400 (Tue, 02 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 554/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEP 1.31.2  (landing page)
Arne Smits
Snapshot Date: 2025-09-01 13:45 -0400 (Mon, 01 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    NA  
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 taishan

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: 1.31.2
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_1.31.2.tar.gz
StartedAt: 2025-09-02 06:05:44 -0000 (Tue, 02 Sep 2025)
EndedAt: 2025-09-02 06:14:32 -0000 (Tue, 02 Sep 2025)
EllapsedTime: 527.4 seconds
RetCode: 0
Status:   OK  
CheckDir: DEP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.31.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/DEP.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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)
* 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 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 ... 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       39.965  0.124  40.220
plot_dist     6.099  0.012   6.132
plot_volcano  5.642  0.076   5.735
* 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-3.22-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-4.5.0/site-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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
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)
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 
 68.203   1.989  70.450 

Example timings

DEP.Rcheck/DEP-Ex.timings

nameusersystemelapsed
LFQ1.8930.0551.955
TMT000
add_rejections1.1650.0001.169
analyze_dep3.9000.0924.005
filter_missval0.6920.0240.719
filter_proteins0.4380.0080.447
get_df_long1.1690.0001.173
get_df_wide1.1190.0041.127
get_prefix0.0030.0000.003
get_results1.4980.0001.503
get_suffix0.0010.0000.002
import_IsobarQuant000
import_MaxQuant0.0750.0000.076
impute39.965 0.12440.220
make_se0.0610.0000.061
make_se_parse0.0910.0000.092
make_unique0.0260.0000.027
manual_impute0.9640.0150.983
meanSdPlot0.8060.0760.885
normalize_vsn0.4770.0000.479
plot_all2.6280.0442.681
plot_cond1.6100.0161.632
plot_cond_freq1.3360.0001.340
plot_cond_overlap1.3280.0001.333
plot_cor1.9250.0041.936
plot_coverage0.7180.0000.721
plot_detect1.1650.0001.169
plot_dist6.0990.0126.132
plot_frequency0.6310.0080.642
plot_gsea1.0510.0001.055
plot_heatmap4.1700.0244.208
plot_imputation1.4980.0161.518
plot_missval2.7060.0322.746
plot_normalization2.2250.0322.265
plot_numbers0.7080.0000.711
plot_p_hist2.0220.0082.038
plot_pca1.8310.0041.841
plot_single2.4540.0032.466
plot_volcano5.6420.0765.735
process2.1610.0322.200
report000
run_app000
se2msn0.2140.0000.214
test_diff1.2680.0041.275
test_gsea1.0440.0001.047
theme_DEP10.6210.0000.623
theme_DEP20.6810.0000.684