Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:06:57 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 tokay2


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 1224/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSPrep 1.4.0  (landing page)
Max McGrath
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/MSPrep
git_branch: RELEASE_3_14
git_last_commit: 34c95d3
git_last_commit_date: 2021-10-26 13:03:21 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MSPrep
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSPrep.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MSPrep_1.4.0.tar.gz
StartedAt: 2022-04-12 23:20:44 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 23:33:07 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 743.8 seconds
RetCode: 0
Status:   OK  
CheckDir: MSPrep.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSPrep.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MSPrep_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MSPrep.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MSPrep/DESCRIPTION' ... OK
* this is package 'MSPrep' version '1.4.0'
* 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 '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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
msImpute    16.61   0.14   16.75
MSPrep      15.86   0.75   16.66
msSummarize 13.86   0.00   13.86
msPrepare   13.08   0.06   13.14
msFilter    12.85   0.12   13.00
msNormalize 12.64   0.03   12.67
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
msImpute    21.42   0.11   21.53
MSPrep      17.54   0.12   17.74
msNormalize 17.45   0.05   17.51
msPrepare   15.85   0.01   15.86
msFilter    14.81   0.08   14.89
msSummarize 13.02   0.04   13.05
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/MSPrep_1.4.0.tar.gz && rm -rf MSPrep.buildbin-libdir && mkdir MSPrep.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MSPrep.buildbin-libdir MSPrep_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL MSPrep_1.4.0.zip && rm MSPrep_1.4.0.tar.gz MSPrep_1.4.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0 1340k    0  5187    0     0  62730      0  0:00:21 --:--:--  0:00:21 62493
 51 1340k   51  686k    0     0   657k      0  0:00:02  0:00:01  0:00:01  657k
100 1340k  100 1340k    0     0   864k      0  0:00:01  0:00:01 --:--:--  864k

install for i386

* installing *source* package 'MSPrep' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MSPrep'
    finding HTML links ... done
    COPD_131                                html  
    MSPrep                                  html  
    msFilter                                html  
    msImpute                                html  
    msNormalize                             html  
    msPrepare                               html  
    msSummarize                             html  
    msquant                                 html  
** 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

install for x64

* installing *source* package 'MSPrep' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MSPrep' as MSPrep_1.4.0.zip
* DONE (MSPrep)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'MSPrep' successfully unpacked and MD5 sums checked

Tests output

MSPrep.Rcheck/tests_i386/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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")


[ FAIL 0 | WARN 0 | SKIP 0 | PASS 84 ]
> 
> 
> proc.time()
   user  system elapsed 
 132.96    2.87  135.92 

MSPrep.Rcheck/tests_x64/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
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.

> Sys.setenv(R_TESTS="")
> library(testthat)
> library(MSPrep)
> 
> test_check("MSPrep")


[ FAIL 0 | WARN 0 | SKIP 0 | PASS 84 ]
> 
> 
> proc.time()
   user  system elapsed 
 141.59    0.89  142.46 

Example timings

MSPrep.Rcheck/examples_i386/MSPrep-Ex.timings

nameusersystemelapsed
COPD_1310.180.020.21
MSPrep15.86 0.7516.66
msFilter12.85 0.1213.00
msImpute16.61 0.1416.75
msNormalize12.64 0.0312.67
msPrepare13.08 0.0613.14
msSummarize13.86 0.0013.86
msquant0.110.000.11

MSPrep.Rcheck/examples_x64/MSPrep-Ex.timings

nameusersystemelapsed
COPD_1310.230.000.23
MSPrep17.54 0.1217.74
msFilter14.81 0.0814.89
msImpute21.42 0.1121.53
msNormalize17.45 0.0517.51
msPrepare15.85 0.0115.86
msSummarize13.02 0.0413.05
msquant0.080.000.07