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CHECK report for CluMSID on tokay2

This page was generated on 2020-10-17 11:56:18 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CluMSID PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 315/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CluMSID 1.4.0
Tobias Depke
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/CluMSID
Branch: RELEASE_3_11
Last Commit: cc91aa9
Last Changed Date: 2020-04-27 15:22:23 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CluMSID
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CluMSID.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings CluMSID_1.4.0.tar.gz
StartedAt: 2020-10-17 02:41:16 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:45:39 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 263.7 seconds
RetCode: 0
Status:  OK  
CheckDir: CluMSID.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CluMSID.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings CluMSID_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/CluMSID.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CluMSID/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CluMSID' 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 'CluMSID' 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
mergeMS2spectra      5.27   0.12    5.39
extractMS2spectra    1.63   0.08    6.87
extractPseudospectra 1.44   0.14    5.45
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
mergeMS2spectra 7.02   0.02    7.03
* 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

CluMSID.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/CluMSID_1.4.0.tar.gz && rm -rf CluMSID.buildbin-libdir && mkdir CluMSID.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CluMSID.buildbin-libdir CluMSID_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL CluMSID_1.4.0.zip && rm CluMSID_1.4.0.tar.gz CluMSID_1.4.0.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 51201  100 51201    0     0   783k      0 --:--:-- --:--:-- --:--:--  892k

install for i386

* installing *source* package 'CluMSID' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CluMSID'
    finding HTML links ... done
    Featurelist                             html  
    HCplot                                  html  
    HCtbl                                   html  
    MDSplot                                 html  
    MS2spectrum-class                       html  
    OPTICSplot                              html  
    OPTICStbl                               html  
    accessors                               html  
    addAnnotations                          html  
    as.MS2spectrum                          html  
    cossim                                  html  
    distanceMatrix                          html  
    extractMS2spectra                       html  
    extractPseudospectra                    html  
    findFragment                            html  
    findNL                                  html  
    getSimilarities                         html  
    getSpectrum                             html  
    mergeMS2spectra                         html  
    mergeSpecList                           html  
    mergeTolerance                          html  
    networkplot                             html  
    neutrallossPatterns                     html  
    pseudospectrum-class                    html  
    specplot                                html  
    splitPolarities                         html  
    writeFeaturelist                        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 'CluMSID' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CluMSID' as CluMSID_1.4.0.zip
* DONE (CluMSID)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'CluMSID' successfully unpacked and MD5 sums checked

Tests output

CluMSID.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(CluMSID)
> 
> test_check("CluMSID")
== testthat results  ===========================================================
[ OK: 16 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  14.73    0.51   15.23 

CluMSID.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(CluMSID)
> 
> test_check("CluMSID")
== testthat results  ===========================================================
[ OK: 16 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  15.92    0.39   16.29 

Example timings

CluMSID.Rcheck/examples_i386/CluMSID-Ex.timings

nameusersystemelapsed
Featurelist0.080.000.28
HCplot0.400.000.57
HCtbl0.010.000.02
MDSplot0.660.040.68
OPTICSplot0.060.000.50
OPTICStbl0.020.010.04
accessors0.080.000.25
addAnnotations0.150.040.58
as.MS2spectrum0.320.000.31
cossim0.030.000.03
distanceMatrix0.920.000.93
extractMS2spectra1.630.086.87
extractPseudospectra1.440.145.45
findFragment0.040.000.05
findNL0.050.000.05
getSimilarities3.950.084.03
getSpectrum0.050.000.05
mergeMS2spectra5.270.125.39
networkplot0.150.000.15
specplot000
splitPolarities1.170.031.21
writeFeaturelist0.020.000.01

CluMSID.Rcheck/examples_x64/CluMSID-Ex.timings

nameusersystemelapsed
Featurelist0.020.000.01
HCplot0.230.000.24
HCtbl0.020.000.01
MDSplot0.900.000.91
OPTICSplot0.010.000.03
OPTICStbl0.020.000.01
accessors0.060.000.07
addAnnotations0.080.030.11
as.MS2spectrum0.170.000.17
cossim0.020.000.01
distanceMatrix0.580.030.61
extractMS2spectra1.390.031.44
extractPseudospectra0.700.050.75
findFragment0.020.000.02
findNL0.030.000.03
getSimilarities2.90.02.9
getSpectrum0.050.000.05
mergeMS2spectra7.020.027.03
networkplot0.150.010.17
specplot0.020.000.02
splitPolarities1.290.031.33
writeFeaturelist0.020.000.01