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CHECK report for MSstatsPTM on tokay1

This page was generated on 2021-05-06 12:32:23 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the MSstatsPTM package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1167/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsPTM 1.0.0  (landing page)
Tsung-Heng Tsai
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/MSstatsPTM
Branch: RELEASE_3_12
Last Commit: d8c642c
Last Changed Date: 2020-10-27 12:01:42 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: MSstatsPTM
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSstatsPTM.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MSstatsPTM_1.0.0.tar.gz
StartedAt: 2021-05-06 04:53:22 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:55:05 -0400 (Thu, 06 May 2021)
EllapsedTime: 102.9 seconds
RetCode: 0
Status:   OK   
CheckDir: MSstatsPTM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSstatsPTM.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MSstatsPTM_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/MSstatsPTM.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MSstatsPTM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MSstatsPTM' version '1.0.0'
* 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 'MSstatsPTM' 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
PTMlocate  3.7   0.23   25.37
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
PTMlocate 2.47   0.11   24.25
* 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

MSstatsPTM.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/MSstatsPTM_1.0.0.tar.gz && rm -rf MSstatsPTM.buildbin-libdir && mkdir MSstatsPTM.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MSstatsPTM.buildbin-libdir MSstatsPTM_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL MSstatsPTM_1.0.0.zip && rm MSstatsPTM_1.0.0.tar.gz MSstatsPTM_1.0.0.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
100 33761  100 33761    0     0  1832k      0 --:--:-- --:--:-- --:--:-- 1939k

install for i386

* installing *source* package 'MSstatsPTM' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MSstatsPTM'
    finding HTML links ... done
    MSstatsPTM                              html  
    PTMcompareMeans                         html  
    PTMestimate                             html  
    PTMlocate                               html  
    PTMnormalize                            html  
    PTMsimulateExperiment                   html  
    PTMsummarize                            html  
    adjustProteinLevel                      html  
    annotSite                               html  
    estimateAbundance                       html  
    extractMeanDiff                         html  
    fitLinearModel                          html  
    fixedGroup                              html  
    fixedGroupBatch                         html  
    locateMod                               html  
    simulatePeaks                           html  
    simulateSites                           html  
    simulateSummarization                   html  
    summarizeFeatures                       html  
    tidyEstimates                           html  
    tidyFasta                               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 'MSstatsPTM' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MSstatsPTM' as MSstatsPTM_1.0.0.zip
* DONE (MSstatsPTM)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'MSstatsPTM' successfully unpacked and MD5 sums checked

Tests output

MSstatsPTM.Rcheck/tests_i386/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.

> library(testthat)
> library(MSstatsPTM)
> 
> test_check("MSstatsPTM")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 40 ]
> 
> proc.time()
   user  system elapsed 
   1.73    0.09    1.81 

MSstatsPTM.Rcheck/tests_x64/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.

> library(testthat)
> library(MSstatsPTM)
> 
> test_check("MSstatsPTM")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 40 ]
> 
> proc.time()
   user  system elapsed 
   1.70    0.15    1.84 

Example timings

MSstatsPTM.Rcheck/examples_i386/MSstatsPTM-Ex.timings

nameusersystemelapsed
PTMcompareMeans0.400.020.42
PTMestimate0.150.000.14
PTMlocate 3.70 0.2325.37
PTMnormalize0.080.000.08
PTMsimulateExperiment0.100.000.09
PTMsummarize0.070.000.08
adjustProteinLevel0.100.020.11
annotSite000
estimateAbundance0.090.000.09
extractMeanDiff0.110.000.11
fitLinearModel0.020.000.02
fixedGroup000
fixedGroupBatch000
locateMod000
simulatePeaks0.030.000.03
simulateSites0.010.000.01
simulateSummarization0.020.000.02
summarizeFeatures0.010.000.01
tidyEstimates0.040.000.03
tidyFasta0.030.000.13

MSstatsPTM.Rcheck/examples_x64/MSstatsPTM-Ex.timings

nameusersystemelapsed
PTMcompareMeans0.30.00.3
PTMestimate0.110.000.11
PTMlocate 2.47 0.1124.25
PTMnormalize0.110.000.11
PTMsimulateExperiment0.180.000.19
PTMsummarize0.150.000.14
adjustProteinLevel0.20.00.2
annotSite000
estimateAbundance0.220.000.22
extractMeanDiff0.250.000.25
fitLinearModel000
fixedGroup000
fixedGroupBatch000
locateMod000
simulatePeaks0.030.000.03
simulateSites0.050.000.05
simulateSummarization0.030.000.03
summarizeFeatures0.040.000.05
tidyEstimates0.050.000.05
tidyFasta0.030.000.12