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CHECK report for MSstatsQC on tokay2

This page was generated on 2019-10-16 12:39:27 -0400 (Wed, 16 Oct 2019).

Package 1059/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsQC 2.2.0
Eralp Dogu
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/MSstatsQC
Branch: RELEASE_3_9
Last Commit: 1144e72
Last Changed Date: 2019-05-02 11:54:08 -0400 (Thu, 02 May 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

Summary

Package: MSstatsQC
Version: 2.2.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSstatsQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MSstatsQC_2.2.0.tar.gz
StartedAt: 2019-10-16 05:26:54 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:32:51 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 357.3 seconds
RetCode: 0
Status:  OK  
CheckDir: MSstatsQC.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSstatsQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MSstatsQC_2.2.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/MSstatsQC.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MSstatsQC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MSstatsQC' version '2.2.0'
* 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 'MSstatsQC' 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 ... NOTE
MissingDataMap: no visible binding for global variable 'AcquiredTime'
MissingDataMap: no visible binding for global variable 'Precursor'
Undefined global functions or variables:
  AcquiredTime Precursor
* 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
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
CUSUMChart           1.54   0.43   21.73
XmRChart             1.20   0.18   37.49
ChangePointEstimator 0.98   0.31   40.31
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/MSstatsQC.Rcheck/00check.log'
for details.



Installation output

MSstatsQC.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/MSstatsQC_2.2.0.tar.gz && rm -rf MSstatsQC.buildbin-libdir && mkdir MSstatsQC.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MSstatsQC.buildbin-libdir MSstatsQC_2.2.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL MSstatsQC_2.2.0.zip && rm MSstatsQC_2.2.0.tar.gz MSstatsQC_2.2.0.zip
###
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  % 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 2519k  100 2519k    0     0  28.2M      0 --:--:-- --:--:-- --:--:-- 30.3M

install for i386

* installing *source* package 'MSstatsQC' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MSstatsQC'
    finding HTML links ... done
    CUSUMChart                              html  
    ChangePointEstimator                    html  
    DataProcess                             html  
    DecisionMap                             html  
    MSnbaseToMSstatsQC                      html  
    MissingDataMap                          html  
    QCloudDDA                               html  
    QCloudSRM                               html  
    QuiCDIA                                 html  
    RadarPlot                               html  
    RemoveMissing                           html  
    RiverPlot                               html  
    S9Site54                                html  
    XmRChart                                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 'MSstatsQC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MSstatsQC' as MSstatsQC_2.2.0.zip
* DONE (MSstatsQC)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'MSstatsQC' successfully unpacked and MD5 sums checked

Tests output

MSstatsQC.Rcheck/tests_i386/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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(MSstatsQC)
> 
> test_check("MSstatsQC")
== testthat results  ===========================================================
[ OK: 15 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   7.00    0.67   10.50 

MSstatsQC.Rcheck/tests_x64/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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(MSstatsQC)
> 
> test_check("MSstatsQC")
== testthat results  ===========================================================
[ OK: 15 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   7.07    0.45    7.54 

Example timings

MSstatsQC.Rcheck/examples_i386/MSstatsQC-Ex.timings

nameusersystemelapsed
CUSUMChart1.430.612.00
ChangePointEstimator0.750.241.05
DataProcess0.030.000.03
DecisionMap2.500.182.71
MissingDataMap000
RadarPlot4.780.104.90
RemoveMissing000
RiverPlot4.060.004.07
XmRChart1.180.311.42

MSstatsQC.Rcheck/examples_x64/MSstatsQC-Ex.timings

nameusersystemelapsed
CUSUMChart 1.54 0.4321.73
ChangePointEstimator 0.98 0.3140.31
DataProcess0.010.000.02
DecisionMap1.970.001.96
MissingDataMap000
RadarPlot3.420.013.44
RemoveMissing000
RiverPlot3.630.003.64
XmRChart 1.20 0.1837.49