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This page was generated on 2021-12-03 13:04:54 -0500 (Fri, 03 Dec 2021).

CHECK results for MSstatsSampleSize on nebbiolo2

To the developers/maintainers of the MSstatsSampleSize package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSstatsSampleSize.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 1234/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsSampleSize 1.8.0  (landing page)
Ting Huang
Snapshot Date: 2021-12-02 01:55:06 -0500 (Thu, 02 Dec 2021)
git_url: https://git.bioconductor.org/packages/MSstatsSampleSize
git_branch: RELEASE_3_14
git_last_commit: 15829c4
git_last_commit_date: 2021-10-26 12:54:51 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: MSstatsSampleSize
Version: 1.8.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:MSstatsSampleSize.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings MSstatsSampleSize_1.8.0.tar.gz
StartedAt: 2021-12-02 08:08:18 -0500 (Thu, 02 Dec 2021)
EndedAt: 2021-12-02 08:10:40 -0500 (Thu, 02 Dec 2021)
EllapsedTime: 142.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MSstatsSampleSize.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:MSstatsSampleSize.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings MSstatsSampleSize_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/MSstatsSampleSize.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstatsSampleSize/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSstatsSampleSize’ version ‘1.8.0’
* 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 ... 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 ... 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    320Kb       xz
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                      user system elapsed
designSampleSizeClassificationPlots 38.937  3.401  22.979
designSampleSizeClassification       8.815  0.117   8.932
* 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: 2 WARNINGs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/MSstatsSampleSize.Rcheck/00check.log’
for details.



Installation output

MSstatsSampleSize.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL MSstatsSampleSize
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MSstatsSampleSize)

Tests output

MSstatsSampleSize.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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(MSstatsSampleSize)
> 
> test_check("MSstatsSampleSize")
[ FAIL 0 | WARN 10 | SKIP 0 | PASS 7 ]
> 
> proc.time()
   user  system elapsed 
 13.456   0.694  14.139 

Example timings

MSstatsSampleSize.Rcheck/MSstatsSampleSize-Ex.timings

nameusersystemelapsed
OV_SRM_train0.0030.0030.007
OV_SRM_train_annotation0.0030.0010.003
classification_results0.0650.0070.073
designSampleSizeClassification8.8150.1178.932
designSampleSizeClassificationPlots38.937 3.40122.979
designSampleSizeHypothesisTestingPlot0.4630.0120.476
designSampleSizePCAplot2.2490.0562.306
estimateVar0.1910.0000.192
meanSDplot1.3190.0201.339
simulateDataset0.2220.0040.225
simulated_datasets0.0170.0000.016
variance_estimation0.0180.0000.017