Back to Build/check report for BioC 3.18:   simplified   long
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This page was generated on 2023-05-31 05:44:33 -0000 (Wed, 31 May 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4219
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CHECK results for DEP on kunpeng1


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.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 524/2197HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEP 1.23.0  (landing page)
Arne Smits
Snapshot Date: 2023-05-29 10:19:22 -0000 (Mon, 29 May 2023)
git_url: https://git.bioconductor.org/packages/DEP
git_branch: devel
git_last_commit: 5f49d82
git_last_commit_date: 2023-04-25 14:55:45 -0000 (Tue, 25 Apr 2023)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    OK    WARNINGS  

Summary

Package: DEP
Version: 1.23.0
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:DEP.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings DEP_1.23.0.tar.gz
StartedAt: 2023-05-30 05:33:32 -0000 (Tue, 30 May 2023)
EndedAt: 2023-05-30 05:43:33 -0000 (Tue, 30 May 2023)
EllapsedTime: 600.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: DEP.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:DEP.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings DEP_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/DEP.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘DEP/DESCRIPTION’ ... OK
* this is package ‘DEP’ version ‘1.23.0’
* 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       71.537  0.363  71.908
plot_volcano  5.255  0.048   5.303
* 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’... OK
  ‘MissingValues.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 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/R/R-4.3.0/bin/R CMD INSTALL DEP
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.0/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 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 
 68.856   1.922  70.790 

Example timings

DEP.Rcheck/DEP-Ex.timings

nameusersystemelapsed
LFQ1.8290.0761.906
TMT000
add_rejections1.1080.0121.120
analyze_dep3.8080.1923.999
filter_missval0.6630.0000.664
filter_proteins0.4140.0030.418
get_df_long1.0930.0001.094
get_df_wide1.8950.0041.900
get_prefix0.0020.0000.003
get_results1.3760.0401.416
get_suffix0.0010.0000.001
import_IsobarQuant000
import_MaxQuant0.0670.0000.068
impute71.537 0.36371.908
make_se0.0670.0080.075
make_se_parse0.0820.0000.083
make_unique0.0230.0000.024
manual_impute0.8750.0160.891
meanSdPlot0.7700.0040.773
normalize_vsn0.4610.0040.465
plot_all2.2460.0042.251
plot_cond1.5550.0001.556
plot_cond_freq1.2350.0001.235
plot_cond_overlap1.2240.0001.224
plot_cor1.6620.0001.662
plot_coverage0.8070.0000.807
plot_detect1.0470.0081.055
plot_dist4.9310.0164.947
plot_frequency0.560.000.56
plot_gsea0.9880.0080.996
plot_heatmap3.7580.0243.781
plot_imputation1.4820.0121.495
plot_missval2.3320.0082.339
plot_normalization1.9470.0161.964
plot_numbers0.730.000.73
plot_p_hist1.8010.0001.800
plot_pca1.9160.0041.920
plot_single2.3160.0042.320
plot_volcano5.2550.0485.303
process1.9860.0001.987
report000
run_app000
se2msn0.1560.0000.156
test_diff1.2820.0001.282
test_gsea0.9940.0040.998
theme_DEP10.6040.0040.608
theme_DEP20.7010.0000.701