Back to Mac ARM64 build report for BioC 3.17
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This page was generated on 2023-10-20 09:38:01 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 532/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEP 1.22.0  (landing page)
Arne Smits
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/DEP
git_branch: RELEASE_3_17
git_last_commit: dfcbed4
git_last_commit_date: 2023-04-25 10:55:45 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for DEP on kjohnson2


To the developers/maintainers of the DEP package:
- 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: 1.22.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DEP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DEP_1.22.0.tar.gz
StartedAt: 2023-10-17 15:08:45 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 15:19:18 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 633.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: DEP.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DEP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DEP_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/DEP.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DEP/DESCRIPTION’ ... OK
* this is package ‘DEP’ version ‘1.22.0’
* 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 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       28.203  0.256  42.672
plot_dist     4.485  0.060   6.862
plot_volcano  4.046  0.062   6.264
* 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
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/DEP.Rcheck/00check.log’
for details.



Installation output

DEP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DEP
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 14 | SKIP 0 | PASS 333 ]

[ FAIL 0 | WARN 14 | SKIP 0 | PASS 333 ]
> 
> proc.time()
   user  system elapsed 
 64.609   3.407 107.846 

Example timings

DEP.Rcheck/DEP-Ex.timings

nameusersystemelapsed
LFQ2.2040.0573.424
TMT000
add_rejections0.8800.0321.400
analyze_dep2.5650.0843.555
filter_missval0.5350.0150.784
filter_proteins0.340.010.46
get_df_long1.5710.0272.296
get_df_wide0.9120.0221.263
get_prefix0.0020.0000.005
get_results1.1640.0281.675
get_suffix0.0010.0000.001
import_IsobarQuant000
import_MaxQuant0.0550.0010.086
impute28.203 0.25642.672
make_se0.0450.0010.070
make_se_parse0.0680.0010.106
make_unique0.0200.0000.032
manual_impute0.8140.0351.315
meanSdPlot0.7280.0431.142
normalize_vsn0.3820.0120.609
plot_all1.9430.0532.966
plot_cond1.3450.0332.095
plot_cond_freq1.0850.0251.703
plot_cond_overlap1.0690.0241.663
plot_cor1.5100.0592.449
plot_coverage0.6960.0181.092
plot_detect1.5860.0292.489
plot_dist4.4850.0606.862
plot_frequency0.4780.0130.764
plot_gsea0.8330.0191.312
plot_heatmap2.9790.0524.587
plot_imputation1.2250.0341.919
plot_missval1.8100.0722.896
plot_normalization1.6140.0472.547
plot_numbers0.6390.0191.002
plot_p_hist1.4910.0302.375
plot_pca1.6800.0292.520
plot_single1.9540.0333.042
plot_volcano4.0460.0626.264
process1.7160.0372.690
report0.0000.0010.001
run_app0.0010.0010.001
se2msn0.1390.0020.221
test_diff1.1060.0271.745
test_gsea0.8180.0191.284
theme_DEP10.5190.0160.803
theme_DEP20.6100.0140.951