Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2024-04-17 11:35:54 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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 540/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEP 1.24.0  (landing page)
Arne Smits
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/DEP
git_branch: RELEASE_3_18
git_last_commit: 3eedbc9
git_last_commit_date: 2023-10-24 10:58:53 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

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: 1.24.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:DEP.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings DEP_1.24.0.tar.gz
StartedAt: 2024-04-15 22:01:55 -0400 (Mon, 15 Apr 2024)
EndedAt: 2024-04-15 22:09:45 -0400 (Mon, 15 Apr 2024)
EllapsedTime: 469.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: DEP.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:DEP.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings DEP_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/DEP.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* 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 ‘1.24.0’
* 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 R 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 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 documentation object 'LFQ.Rd':
  ‘[MSnbase:impute-methods]{impute}’

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

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

Missing link or links in documentation object '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 51.305  0.528  51.833
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘DEP.Rmd’ using ‘UTF-8’... failed
  ‘MissingValues.Rmd’ using ‘UTF-8’... failed
 ERROR
Errors in running code in vignettes:
when running code in ‘DEP.Rmd’
  ...

> plot_missval(data_filt)

> plot_detect(data_filt)

> impute(data_norm, fun = "")

  When sourcing ‘DEP.R’:
Error: 'arg' should be one of “bpca”, “knn”, “QRILC”, “MLE”, “MinDet”, “MinProb”, “man”, “min”, “zero”, “mixed”, “nbavg”
Execution halted
when running code in ‘MissingValues.Rmd’
  ...

> plot_missval(no_filter)

> plot_detect(no_filter)

> impute(no_filter, fun = "")

  When sourcing ‘MissingValues.R’:
Error: 'arg' should be one of “bpca”, “knn”, “QRILC”, “MLE”, “MinDet”, “MinProb”, “man”, “min”, “zero”, “mixed”, “nbavg”
Execution halted

* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/DEP.Rcheck/00check.log’
for details.


Installation output

DEP.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL DEP
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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 
 46.742   1.591  48.343 

Example timings

DEP.Rcheck/DEP-Ex.timings

nameusersystemelapsed
LFQ1.7660.0801.846
TMT0.0000.0000.001
add_rejections0.6800.0360.716
analyze_dep2.4680.1162.585
filter_missval0.4020.0120.414
filter_proteins0.2510.0000.251
get_df_long0.6910.0040.695
get_df_wide0.6680.0200.688
get_prefix0.0000.0020.002
get_results0.8680.0610.930
get_suffix0.0010.0000.001
import_IsobarQuant000
import_MaxQuant0.0440.0000.045
impute51.305 0.52851.833
make_se0.0480.0120.060
make_se_parse0.0540.0000.053
make_unique0.0160.0000.015
manual_impute0.5770.0120.589
meanSdPlot0.5060.0120.518
normalize_vsn0.2980.0000.298
plot_all1.5320.0121.545
plot_cond0.9290.0000.929
plot_cond_freq0.7910.0000.791
plot_cond_overlap0.810.000.81
plot_cor1.090.001.09
plot_coverage0.4230.0000.423
plot_detect0.6250.0000.626
plot_dist3.1790.0083.187
plot_frequency0.3710.0000.371
plot_gsea0.6220.0080.630
plot_heatmap2.3530.0002.353
plot_imputation0.9080.0040.912
plot_missval1.4070.0121.421
plot_normalization1.1890.0001.189
plot_numbers0.4180.0000.419
plot_p_hist1.1230.0001.124
plot_pca1.0830.0041.087
plot_single1.4500.0441.494
plot_volcano3.8550.0283.884
process1.2520.0001.252
report0.0010.0000.000
run_app000
se2msn0.1050.0000.104
test_diff0.8180.0040.823
test_gsea0.670.000.67
theme_DEP10.3610.0000.360
theme_DEP20.4350.0000.434