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CHECK report for BioCor on tokay1

This page was generated on 2019-04-13 11:27:39 -0400 (Sat, 13 Apr 2019).

Package 141/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioCor 1.6.1
LluĂ­s Revilla Sancho
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/BioCor
Branch: RELEASE_3_8
Last Commit: 421f8ca
Last Changed Date: 2019-02-02 10:35:57 -0400 (Sat, 02 Feb 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BioCor
Version: 1.6.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioCor.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings BioCor_1.6.1.tar.gz
StartedAt: 2019-04-13 00:47:23 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 00:51:10 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 227.1 seconds
RetCode: 0
Status:  OK  
CheckDir: BioCor.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioCor.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings BioCor_1.6.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/BioCor.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BioCor/DESCRIPTION' ... OK
* this is package 'BioCor' version '1.6.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'BioCor' 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 R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'spelling.R'
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'spelling.R'
  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

BioCor.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/BioCor_1.6.1.tar.gz && rm -rf BioCor.buildbin-libdir && mkdir BioCor.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BioCor.buildbin-libdir BioCor_1.6.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL BioCor_1.6.1.zip && rm BioCor_1.6.1.tar.gz BioCor_1.6.1.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 53635  100 53635    0     0  1285k      0 --:--:-- --:--:-- --:--:-- 1415k

install for i386

* installing *source* package 'BioCor' ...
** R
** byte-compile and prepare package for lazy loading
Creating a generic function from function 'clusterGeneSim' in package 'BioCor'
Creating a generic function from function 'clusterSim' in package 'BioCor'
Creating a generic function from function 'geneSim' in package 'BioCor'
Creating a generic function from function 'mclusterGeneSim' in package 'BioCor'
Creating a generic function from function 'mclusterSim' in package 'BioCor'
Creating a generic function from function 'mgeneSim' in package 'BioCor'
Creating a generic function from function 'mpathSim' in package 'BioCor'
Creating a generic function from function 'pathSim' in package 'BioCor'
** help
*** installing help indices
  converting help for package 'BioCor'
    finding HTML links ... done
    AintoB                                  html  
    BioCor-package                          html  
    addSimilarities                         html  
    clusterGeneSim                          html  
    clusterSim                              html  
    combinadic                              html  
    combineScores                           html  
    combineSources                          html  
    conversions                             html  
    diceSim                                 html  
    duplicateIndices                        html  
    geneSim                                 html  
    incidence-list-method                   html  
    inverseList                             html  
    mclusterGeneSim                         html  
    mclusterSim                             html  
    mgeneSim                                html  
    mpathSim                                html  
    pathSim                                 html  
    removeDup                               html  
    seq2mat                                 html  
    similarities                            html  
    weighted                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'BioCor' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BioCor' as BioCor_1.6.1.zip
* DONE (BioCor)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'BioCor' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

BioCor.Rcheck/tests_i386/spelling.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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.

> if(requireNamespace('spelling', quietly=TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE, skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
   0.12    0.03    0.28 

BioCor.Rcheck/tests_x64/spelling.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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.

> if(requireNamespace('spelling', quietly=TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE, skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
   0.14    0.03    0.17 

BioCor.Rcheck/tests_i386/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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(BioCor)
If you use BioCor in published research, please cite:
> 
> test_check("BioCor")
== testthat results  ===========================================================
OK: 322 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   8.45    0.50    9.01 

BioCor.Rcheck/tests_x64/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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(BioCor)
If you use BioCor in published research, please cite:
> 
> test_check("BioCor")
== testthat results  ===========================================================
OK: 322 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  10.64    0.29   10.92 

Example timings

BioCor.Rcheck/examples_i386/BioCor-Ex.timings

nameusersystemelapsed
AintoB000
addSimilarities0.010.000.02
clusterGeneSim1.020.201.22
clusterSim0.530.050.58
combinadic000
combineScores000
combineSources000
conversions000
diceSim000
duplicateIndices000
geneSim2.530.092.63
mclusterGeneSim0.810.000.81
mclusterSim0.890.030.92
mgeneSim3.140.023.16
mpathSim3.120.043.17
pathSim2.180.042.20
removeDup000
seq2mat000
similarities000
weighted000

BioCor.Rcheck/examples_x64/BioCor-Ex.timings

nameusersystemelapsed
AintoB000
addSimilarities0.020.000.02
clusterGeneSim1.390.051.43
clusterSim0.610.000.61
combinadic000
combineScores000
combineSources000
conversions000
diceSim000
duplicateIndices000
geneSim3.040.073.13
mclusterGeneSim0.750.040.78
mclusterSim0.600.010.61
mgeneSim2.500.172.67
mpathSim2.870.082.95
pathSim2.250.062.31
removeDup000
seq2mat000
similarities000
weighted000