Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
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 536/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEP 1.27.0  (landing page)
Arne Smits
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/DEP
git_branch: devel
git_last_commit: 7fcd1ce
git_last_commit_date: 2024-04-30 10:59:44 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  


CHECK results for DEP on palomino6

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: 1.27.0
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DEP.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings DEP_1.27.0.tar.gz
StartedAt: 2024-07-15 23:25:20 -0400 (Mon, 15 Jul 2024)
EndedAt: 2024-07-15 23:31:55 -0400 (Mon, 15 Jul 2024)
EllapsedTime: 395.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: DEP.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DEP.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings DEP_1.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/DEP.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'DEP/DESCRIPTION' ... OK
* this is package 'DEP' version '1.27.0'
* 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 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 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 38.11   0.25   38.38
* 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
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/DEP.Rcheck/00check.log'
for details.


Installation output

DEP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL DEP
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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")
pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
[ FAIL 0 | WARN 14 | SKIP 0 | PASS 333 ]

[ FAIL 0 | WARN 14 | SKIP 0 | PASS 333 ]
> 
> proc.time()
   user  system elapsed 
  44.06    2.57   66.92 

Example timings

DEP.Rcheck/DEP-Ex.timings

nameusersystemelapsed
LFQ2.060.032.09
TMT000
add_rejections0.640.020.66
analyze_dep1.630.091.73
filter_missval0.340.000.35
filter_proteins0.200.000.21
get_df_long0.660.020.67
get_df_wide0.610.030.64
get_prefix000
get_results1.700.001.71
get_suffix000
import_IsobarQuant000
import_MaxQuant0.030.000.03
impute38.11 0.2538.38
make_se0.030.000.04
make_se_parse0.060.030.09
make_unique0.020.000.02
manual_impute0.470.040.51
meanSdPlot0.640.100.74
normalize_vsn0.370.000.37
plot_all1.280.011.30
plot_cond0.860.030.89
plot_cond_freq0.740.000.74
plot_cond_overlap0.750.040.78
plot_cor1.170.281.11
plot_coverage0.440.110.36
plot_detect0.540.010.56
plot_dist3.660.133.78
plot_frequency0.310.000.31
plot_gsea0.590.000.60
plot_heatmap2.060.032.14
plot_imputation0.770.040.81
plot_missval1.590.111.70
plot_normalization1.100.131.22
plot_numbers0.370.050.38
plot_p_hist1.050.031.08
plot_pca1.080.001.07
plot_single1.250.031.29
plot_volcano3.370.033.42
process1.110.031.14
report000
run_app000
se2msn0.100.000.09
test_diff0.820.050.86
test_gsea0.610.000.61
theme_DEP10.320.010.32
theme_DEP20.390.000.39