Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:21:23 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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

CHECK results for DEP on palomino3


To the developers/maintainers of the DEP package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 506/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEP 1.18.0  (landing page)
Arne Smits
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/DEP
git_branch: RELEASE_3_15
git_last_commit: 5609377
git_last_commit_date: 2022-04-26 11:42:30 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 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 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: DEP
Version: 1.18.0
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DEP.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings DEP_1.18.0.tar.gz
StartedAt: 2022-10-18 23:35:11 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 23:41:14 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 363.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: DEP.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DEP.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings DEP_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/DEP.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'DEP/DESCRIPTION' ... OK
* this is package 'DEP' version '1.18.0'
* 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 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 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
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  'F:/biocbuild/bbs-3.15-bioc/meat/DEP.Rcheck/00check.log'
for details.



Installation output

DEP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL DEP
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-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 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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")
!!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
!!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
!!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
!!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
!!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
!!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
!!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
!!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
!!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
!!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)!
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 
  47.76    1.67   64.71 

Example timings

DEP.Rcheck/DEP-Ex.timings

nameusersystemelapsed
LFQ1.670.061.82
TMT000
add_rejections1.530.021.54
analyze_dep1.980.001.99
filter_missval0.520.030.54
filter_proteins0.470.000.47
get_df_long1.010.001.02
get_df_wide0.820.030.84
get_prefix000
get_results1.930.031.97
get_suffix000
import_IsobarQuant000
import_MaxQuant0.070.000.06
impute1.250.011.31
make_se0.040.000.05
make_se_parse0.050.000.04
make_unique0.020.000.02
manual_impute0.760.000.77
meanSdPlot0.670.030.71
normalize_vsn0.610.000.61
plot_all1.720.021.74
plot_cond1.200.021.30
plot_cond_freq0.890.000.89
plot_cond_overlap1.150.011.15
plot_cor1.540.001.74
plot_coverage0.770.020.78
plot_detect0.780.000.78
plot_dist4.160.044.22
plot_frequency0.580.000.58
plot_gsea1.010.001.02
plot_heatmap3.150.003.14
plot_imputation1.030.031.06
plot_missval1.820.001.83
plot_normalization1.650.021.65
plot_numbers0.840.000.84
plot_p_hist1.610.021.63
plot_pca1.630.031.67
plot_single2.870.042.92
plot_volcano4.520.074.72
process1.470.001.47
report000
run_app000
se2msn0.140.000.14
test_diff1.030.001.03
test_gsea0.910.030.94
theme_DEP10.480.000.48
theme_DEP20.520.000.52