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This page was generated on 2025-09-15 12:03 -0400 (Mon, 15 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4719
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4538
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4522
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4543
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 557/2327HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEP 1.31.2  (landing page)
Arne Smits
Snapshot Date: 2025-09-14 13:45 -0400 (Sun, 14 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 nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:DEP.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings DEP_1.31.2.tar.gz
StartedAt: 2025-09-14 23:00:47 -0400 (Sun, 14 Sep 2025)
EndedAt: 2025-09-14 23:11:20 -0400 (Sun, 14 Sep 2025)
EllapsedTime: 632.8 seconds
RetCode: 0
Status:   OK  
CheckDir: DEP.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:DEP.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings DEP_1.31.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/DEP.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 54.768  0.449   55.31
* 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 re-building of vignette outputs ... OK
* 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/bbs-3.22-bioc/R/bin/R CMD INSTALL DEP
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 16 | SKIP 0 | PASS 333 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 333 ]
> 
> proc.time()
   user  system elapsed 
 58.093   2.176  60.289 

Example timings

DEP.Rcheck/DEP-Ex.timings

nameusersystemelapsed
LFQ1.3220.0181.340
TMT000
add_rejections1.5690.0831.652
analyze_dep2.1110.1372.248
filter_missval0.4160.0370.453
filter_proteins0.2510.0090.260
get_df_long0.7000.0080.708
get_df_wide0.7080.0040.712
get_prefix0.0020.0000.002
get_results0.8900.0080.898
get_suffix0.0010.0000.002
import_IsobarQuant000
import_MaxQuant0.0460.0000.046
impute54.768 0.44955.310
make_se0.0340.0020.037
make_se_parse0.0540.0020.057
make_unique0.0170.0000.017
manual_impute0.6280.0170.645
meanSdPlot0.6390.0020.641
normalize_vsn0.3290.0000.329
plot_all1.8360.0011.837
plot_cond1.1120.0021.114
plot_cond_freq0.9430.0000.942
plot_cond_overlap0.880.000.88
plot_cor1.1670.0001.167
plot_coverage0.5610.0000.562
plot_detect0.9090.0000.909
plot_dist3.4520.0143.466
plot_frequency0.4940.0130.507
plot_gsea0.6400.0090.649
plot_heatmap2.4110.0242.435
plot_imputation1.1050.0071.112
plot_missval1.4910.0041.495
plot_normalization1.5140.0381.552
plot_numbers0.5870.0050.592
plot_p_hist1.3610.0061.367
plot_pca1.3910.0391.431
plot_single2.0110.0292.041
plot_volcano4.5220.0334.561
process1.5890.0101.599
report000
run_app000
se2msn0.1120.0000.112
test_diff0.8410.0000.841
test_gsea0.6590.0010.660
theme_DEP10.4870.0010.487
theme_DEP20.5850.0020.587