Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:20:34 -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 MSPrep on nebbiolo1


To the developers/maintainers of the MSPrep package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSPrep.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 1256/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSPrep 1.6.0  (landing page)
Max McGrath
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/MSPrep
git_branch: RELEASE_3_15
git_last_commit: 4f27af9
git_last_commit_date: 2022-04-26 12:09:02 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MSPrep
Version: 1.6.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:MSPrep.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings MSPrep_1.6.0.tar.gz
StartedAt: 2022-10-18 20:44:37 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 20:51:05 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 388.8 seconds
RetCode: 0
Status:   OK  
CheckDir: MSPrep.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:MSPrep.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings MSPrep_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/MSPrep.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSPrep/DESCRIPTION’ ... OK
* this is package ‘MSPrep’ version ‘1.6.0’
* 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 ‘MSPrep’ 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 ... 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
MSPrep      16.004  0.557  16.576
msImpute    15.481  0.264  15.745
msPrepare   13.150  0.200  13.362
msFilter    11.682  0.208  11.890
msNormalize 11.351  0.116  11.468
msSummarize  9.860  0.060   9.926
* 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: OK


Installation output

MSPrep.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL MSPrep
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘MSPrep’ ...
** using staged installation
** R
** data
** 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 (MSPrep)

Tests output

MSPrep.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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.

> Sys.setenv(R_TESTS="")
> library(testthat)
> library(MSPrep)
> 
> test_check("MSPrep")
Number of significant surrogate variables is:  4 
Iteration (out of 5 ):1  2  3  4  5  Found 7 genes with uniform expression within a single batch (all zeros); these will not be adjusted for batch.
Number of significant surrogate variables is:  4 
Iteration (out of 5 ):1  2  3  4  5  
Number of significant surrogate variables is:  4 
Iteration (out of 5 ):1  2  3  4  5  Found 7 genes with uniform expression within a single batch (all zeros); these will not be adjusted for batch.
Number of significant surrogate variables is:  4 
Iteration (out of 5 ):1  2  3  4  5  
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 84 ]

[ FAIL 0 | WARN 11 | SKIP 0 | PASS 84 ]
> 
> 
> proc.time()
   user  system elapsed 
127.976   2.002 129.960 

Example timings

MSPrep.Rcheck/MSPrep-Ex.timings

nameusersystemelapsed
COPD_1310.1860.0010.185
MSPrep16.004 0.55716.576
msFilter11.682 0.20811.890
msImpute15.481 0.26415.745
msNormalize11.351 0.11611.468
msPrepare13.150 0.20013.362
msSummarize9.8600.0609.926
msquant0.0760.0000.076