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This page was generated on 2025-03-17 11:40 -0400 (Mon, 17 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4459
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 549/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEP 1.29.0  (landing page)
Arne Smits
Snapshot Date: 2025-03-16 13:40 -0400 (Sun, 16 Mar 2025)
git_url: https://git.bioconductor.org/packages/DEP
git_branch: devel
git_last_commit: 44e537d
git_last_commit_date: 2024-10-29 10:21:24 -0400 (Tue, 29 Oct 2024)
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 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 kjohnson3

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: 1.29.0
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_1.29.0.tar.gz
StartedAt: 2025-03-16 19:03:02 -0400 (Sun, 16 Mar 2025)
EndedAt: 2025-03-16 19:05:26 -0400 (Sun, 16 Mar 2025)
EllapsedTime: 144.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: DEP.Rcheck
Warnings: 1

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_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/DEP.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DEP/DESCRIPTION’ ... OK
* this is package ‘DEP’ version ‘1.29.0’
* 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 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 5.055  0.034   5.092
* 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
  ‘/Users/biocbuild/bbs-3.21-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-arm64/Resources/library’
* installing *source* package ‘DEP’ ...
** this is package ‘DEP’ version ‘1.29.0’
** 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) (2025-03-02 r87868) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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)
> 
> test_check("DEP")
[ FAIL 0 | WARN 14 | SKIP 0 | PASS 333 ]

[ FAIL 0 | WARN 14 | SKIP 0 | PASS 333 ]
> 
> proc.time()
   user  system elapsed 
 18.544   0.967  19.782 

Example timings

DEP.Rcheck/DEP-Ex.timings

nameusersystemelapsed
LFQ0.4080.0180.426
TMT000
add_rejections0.2330.0060.241
analyze_dep0.9770.0221.000
filter_missval0.1430.0040.147
filter_proteins0.0840.0010.086
get_df_long0.2290.0120.241
get_df_wide0.6080.0150.630
get_prefix0.0010.0000.001
get_results0.2870.0120.298
get_suffix000
import_IsobarQuant000
import_MaxQuant0.0160.0000.016
impute5.0550.0345.092
make_se0.0130.0010.013
make_se_parse0.0180.0000.018
make_unique0.0060.0010.007
manual_impute0.5610.0060.567
meanSdPlot0.2200.0080.229
normalize_vsn0.1000.0020.100
plot_all0.4450.0080.453
plot_cond0.3060.0040.311
plot_cond_freq0.2520.0030.256
plot_cond_overlap0.2560.0050.260
plot_cor0.3870.0070.394
plot_coverage0.1430.0010.144
plot_detect0.2140.0010.214
plot_dist1.1130.0081.122
plot_frequency0.1200.0030.125
plot_gsea0.2060.0050.211
plot_heatmap0.7930.0180.813
plot_imputation0.3030.0100.314
plot_missval0.4940.0440.547
plot_normalization0.3940.0170.424
plot_numbers0.1540.0020.157
plot_p_hist0.3840.0080.394
plot_pca0.3750.0080.413
plot_single0.4700.0090.480
plot_volcano1.7280.0141.743
process0.4260.0080.434
report000
run_app000
se2msn0.0480.0010.048
test_diff0.2730.0080.281
test_gsea0.2440.0130.258
theme_DEP10.1300.0020.132
theme_DEP20.1520.0030.156