Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-06-28 17:39 -0400 (Fri, 28 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4760
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4494
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4508
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4362
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 549/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEP 1.26.0  (landing page)
Arne Smits
Snapshot Date: 2024-06-26 14:00 -0400 (Wed, 26 Jun 2024)
git_url: https://git.bioconductor.org/packages/DEP
git_branch: RELEASE_3_19
git_last_commit: cca9bde
git_last_commit_date: 2024-04-30 10:59:44 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 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
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  


CHECK results for DEP on nebbiolo1

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: 1.26.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:DEP.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings DEP_1.26.0.tar.gz
StartedAt: 2024-06-26 22:28:42 -0400 (Wed, 26 Jun 2024)
EndedAt: 2024-06-26 22:36:43 -0400 (Wed, 26 Jun 2024)
EllapsedTime: 480.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: DEP.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:DEP.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings DEP_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/DEP.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘DEP/DESCRIPTION’ ... OK
* this is package ‘DEP’ version ‘1.26.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 or links in Rd file 'LFQ.Rd':
  ‘[MSnbase:impute-methods]{impute}’

Missing link or links in Rd file 'TMT.Rd':
  ‘[MSnbase:impute-methods]{impute}’

Missing link or links in Rd file 'impute.Rd':
  ‘[MSnbase:impute-methods]{impute}’

Missing link or links 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 53.611  0.423  54.037
* 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 WARNING
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/DEP.Rcheck/00check.log’
for details.


Installation output

DEP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL DEP
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘DEP’ ...
** 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 version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 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)
> 
> test_check("DEP")
[ FAIL 0 | WARN 15 | SKIP 0 | PASS 333 ]

[ FAIL 0 | WARN 15 | SKIP 0 | PASS 333 ]
> 
> proc.time()
   user  system elapsed 
 48.981   1.979  50.970 

Example timings

DEP.Rcheck/DEP-Ex.timings

nameusersystemelapsed
LFQ2.030.062.09
TMT000
add_rejections0.6730.0210.694
analyze_dep1.8860.0431.930
filter_missval0.4120.0040.415
filter_proteins0.2540.0000.255
get_df_long1.6040.1391.744
get_df_wide0.6550.0040.660
get_prefix0.0020.0000.002
get_results0.8470.0390.887
get_suffix0.0010.0000.002
import_IsobarQuant0.0010.0010.000
import_MaxQuant0.0520.0000.052
impute53.611 0.42354.037
make_se0.0270.0080.036
make_se_parse0.0590.0080.067
make_unique0.0160.0000.015
manual_impute0.5690.0040.573
meanSdPlot0.5050.0800.586
normalize_vsn0.2970.0200.317
plot_all1.5140.0161.529
plot_cond0.9680.0120.981
plot_cond_freq0.7960.0000.796
plot_cond_overlap0.7720.0000.771
plot_cor1.140.001.14
plot_coverage0.4020.0000.401
plot_detect0.6720.0000.671
plot_dist3.3260.0123.338
plot_frequency0.3530.0000.354
plot_gsea0.6560.0280.685
plot_heatmap2.2920.0002.293
plot_imputation0.9210.0000.920
plot_missval1.4410.0441.485
plot_normalization2.0840.1322.216
plot_numbers0.4080.0080.417
plot_p_hist1.0860.0041.090
plot_pca1.0800.0001.082
plot_single1.4050.0441.449
plot_volcano3.8720.0163.887
process1.2810.0081.288
report0.0010.0000.000
run_app000
se2msn0.1100.0000.111
test_diff0.8170.0360.853
test_gsea0.6310.0240.655
theme_DEP10.3890.0080.397
theme_DEP20.390.000.39