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This page was generated on 2024-04-18 11:32:14 -0400 (Thu, 18 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4388
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Package 1350/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsSampleSize 1.16.0  (landing page)
Ting Huang
Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024)
git_url: https://git.bioconductor.org/packages/MSstatsSampleSize
git_branch: RELEASE_3_18
git_last_commit: c984b87
git_last_commit_date: 2023-10-24 11:16:56 -0400 (Tue, 24 Oct 2023)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for MSstatsSampleSize on kjohnson1


To the developers/maintainers of the MSstatsSampleSize 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: MSstatsSampleSize
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsSampleSize.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsSampleSize_1.16.0.tar.gz
StartedAt: 2024-04-17 20:48:15 -0400 (Wed, 17 Apr 2024)
EndedAt: 2024-04-17 20:50:56 -0400 (Wed, 17 Apr 2024)
EllapsedTime: 161.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MSstatsSampleSize.Rcheck
Warnings: 3

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsSampleSize.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsSampleSize_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/MSstatsSampleSize.Rcheck’
* using R version 4.3.3 (2024-02-29)
* 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 Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstatsSampleSize/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSstatsSampleSize’ version ‘1.16.0’
* 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 ‘MSstatsSampleSize’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'MSstatsSampleSize' is deprecated and will be removed from
See ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/MSstatsSampleSize.Rcheck/00install.out’ for details.
* 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 ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Functions or methods with usage in documentation object '.classification' but not in code:
  ‘.classification’

* 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                             old_size new_size compress
  classification_results.rda    1.8Mb    1.3Mb       xz
  simulated_datasets.rda        656Kb    511Kb       xz
  variance_estimation.rda       690Kb    321Kb       xz
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                      user system elapsed
designSampleSizeClassificationPlots 20.110  2.590  13.538
designSampleSizeClassification       5.349  0.108   5.473
* 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: 3 WARNINGs
See
  ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/MSstatsSampleSize.Rcheck/00check.log’
for details.



Installation output

MSstatsSampleSize.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘MSstatsSampleSize’ ...
** 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
Warning: Package 'MSstatsSampleSize' is deprecated and will be removed from
  Bioconductor version 3.19
** testing if installed package can be loaded from final location
Warning: Package 'MSstatsSampleSize' is deprecated and will be removed from
  Bioconductor version 3.19
** testing if installed package keeps a record of temporary installation path
* DONE (MSstatsSampleSize)

Tests output

MSstatsSampleSize.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: 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(MSstatsSampleSize)
Warning message:
Package 'MSstatsSampleSize' is deprecated and will be removed from
  Bioconductor version 3.19 
> 
> test_check("MSstatsSampleSize")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 7 ]
> 
> proc.time()
   user  system elapsed 
 10.229   0.478  10.699 

Example timings

MSstatsSampleSize.Rcheck/MSstatsSampleSize-Ex.timings

nameusersystemelapsed
OV_SRM_train0.0050.0090.013
OV_SRM_train_annotation0.0040.0000.004
classification_results0.1520.0070.159
designSampleSizeClassification5.3490.1085.473
designSampleSizeClassificationPlots20.110 2.59013.538
designSampleSizeHypothesisTestingPlot0.2620.0270.289
designSampleSizePCAplot2.5150.0882.605
estimateVar0.2120.0160.228
meanSDplot1.6430.0841.728
simulateDataset0.2390.0220.261
simulated_datasets0.0210.0030.025
variance_estimation0.0290.0020.030