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CHECK report for MSstatsTMT on tokay2

This page was generated on 2019-04-09 12:42:24 -0400 (Tue, 09 Apr 2019).

Package 1043/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsTMT 1.1.2
Ting Huang
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/MSstatsTMT
Branch: master
Last Commit: 5f454a7
Last Changed Date: 2019-02-25 14:20:12 -0400 (Mon, 25 Feb 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: MSstatsTMT
Version: 1.1.2
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSstatsTMT.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MSstatsTMT_1.1.2.tar.gz
StartedAt: 2019-04-09 04:28:07 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 04:32:14 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 247.1 seconds
RetCode: 0
Status:  OK  
CheckDir: MSstatsTMT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSstatsTMT.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MSstatsTMT_1.1.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/MSstatsTMT.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MSstatsTMT/DESCRIPTION' ... OK
* this is package 'MSstatsTMT' version '1.1.2'
* 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 'MSstatsTMT' 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 or elapsed time > 5s
                      user system elapsed
dataProcessPlotsTMT  43.69   0.72   44.43
groupComparisonTMT    7.68   0.39    8.00
proteinSummarization  6.99   0.38    7.27
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
dataProcessPlotsTMT  43.52   0.57   45.95
groupComparisonTMT    7.85   0.31    8.19
proteinSummarization  6.34   0.22    6.31
* 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

MSstatsTMT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/MSstatsTMT_1.1.2.tar.gz && rm -rf MSstatsTMT.buildbin-libdir && mkdir MSstatsTMT.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MSstatsTMT.buildbin-libdir MSstatsTMT_1.1.2.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL MSstatsTMT_1.1.2.zip && rm MSstatsTMT_1.1.2.tar.gz MSstatsTMT_1.1.2.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
 10 1080k   10  112k    0     0   543k      0  0:00:01 --:--:--  0:00:01  560k
100 1080k  100 1080k    0     0  1968k      0 --:--:-- --:--:-- --:--:-- 1990k

install for i386

* installing *source* package 'MSstatsTMT' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MSstatsTMT'
    finding HTML links ... done
    MSstatsTMT                              html  
    MaxQtoMSstatsTMTFormat                  html  
    PDtoMSstatsTMTFormat                    html  
    SpectroMinetoMSstatsTMTFormat           html  
    annotation.mine                         html  
    annotation.mq                           html  
    annotation.pd                           html  
    dataProcessPlotsTMT                     html  
    evidence                                html  
    groupComparisonTMT                      html  
    input.pd                                html  
    proteinGroups                           html  
    proteinSummarization                    html  
    quant.pd.msstats                        html  
    raw.mine                                html  
    raw.pd                                  html  
    test.pairwise                           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 'MSstatsTMT' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MSstatsTMT' as MSstatsTMT_1.1.2.zip
* DONE (MSstatsTMT)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'MSstatsTMT' successfully unpacked and MD5 sums checked

Tests output

MSstatsTMT.Rcheck/tests_i386/testthat.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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(MSstatsTMT)
> 
> test_check("MSstatsTMT")
                       
  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     4-29
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     3-33
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     3-29
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     1-28
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     1-30
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     2-30
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     4-31
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     3-30
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     5-30
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     3-31
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     3-31
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     1-31
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     3-34
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     2-30
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     5-32
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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== testthat results  ===========================================================
OK: 33 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   9.89    0.89   10.51 

MSstatsTMT.Rcheck/tests_x64/testthat.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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(MSstatsTMT)
> 
> test_check("MSstatsTMT")
                       
  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     4-29
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     3-33
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     3-29
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     1-28
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     1-30
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     2-30
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     4-31
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     3-30
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     5-30
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     3-31
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     3-31
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     1-31
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     3-34
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     2-30
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     5-32
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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== testthat results  ===========================================================
OK: 33 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  10.56    0.82   11.36 

Example timings

MSstatsTMT.Rcheck/examples_i386/MSstatsTMT-Ex.timings

nameusersystemelapsed
MaxQtoMSstatsTMTFormat0.660.120.64
PDtoMSstatsTMTFormat0.810.020.83
SpectroMinetoMSstatsTMTFormat0.410.060.47
annotation.mine000
annotation.mq000
annotation.pd000
dataProcessPlotsTMT43.69 0.7244.43
evidence0.010.030.04
groupComparisonTMT7.680.398.00
input.pd000
proteinGroups0.100.090.18
proteinSummarization6.990.387.27
quant.pd.msstats000
raw.mine0.010.000.01
raw.pd0.020.000.02
test.pairwise000

MSstatsTMT.Rcheck/examples_x64/MSstatsTMT-Ex.timings

nameusersystemelapsed
MaxQtoMSstatsTMTFormat0.700.230.75
PDtoMSstatsTMTFormat1.160.021.17
SpectroMinetoMSstatsTMTFormat0.590.040.65
annotation.mine000
annotation.mq000
annotation.pd000
dataProcessPlotsTMT43.52 0.5745.95
evidence0.040.010.02
groupComparisonTMT7.850.318.19
input.pd0.010.000.01
proteinGroups0.080.100.13
proteinSummarization6.340.226.31
quant.pd.msstats000
raw.mine0.020.000.02
raw.pd000
test.pairwise000