Multiple platform build/check report for BioC 3.9 - CHECK report for rqt on tokay2

Package: rqt

Version: 1.10.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rqt.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings rqt_1.10.0.tar.gz

StartedAt: 2019-10-16 06:47:14 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 06:50:35 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 201.0 seconds

RetCode: 0

Status: OK

CheckDir: rqt.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rqt.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings rqt_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/rqt.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 'rqt/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rqt' version '1.10.0'
* 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 'rqt' 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 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/rqt_1.10.0.tar.gz && rm -rf rqt.buildbin-libdir && mkdir rqt.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rqt.buildbin-libdir rqt_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL rqt_1.10.0.zip && rm rqt_1.10.0.tar.gz rqt_1.10.0.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  374k  100  374k    0     0  2362k      0 --:--:-- --:--:-- --:--:-- 2463k

install for i386

* installing *source* package 'rqt' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'rqt'
    finding HTML links ... done
    build.null.model                        html  
    get.a                                   html  
    preprocess                              html  
    rqt-class                               html  
    rqt-covariates                          html  
    rqt-geneTest                            html  
    rqt-geneTestMeta                        html  
    rqt-general                             html  
    rqt-genotype                            html  
    rqt-methods                             html  
    rqt-phenotype                           html  
    rqt-results                             html  
    simple.multvar.reg                      html  
    vcov_ridge                              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 'rqt' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rqt' as rqt_1.10.0.zip
* DONE (rqt)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'rqt' successfully unpacked and MD5 sums checked


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.

> # Adapted from: http://rwiki.sciviews.org/doku.php?id=developers:runit
> 
> if( identical( .Platform$OS.type, "windows" ) && 
+     identical( .Platform$r_arch, "x64" ) ){
+   print( "unit tests not run on windows 64 (workaround alert)" )
+ } else {
+   if(require("RUnit", quietly = TRUE)) {
+     pkg <- "rqt"
+     if(Sys.getenv("RCMDCHECK") == "FALSE") {
+       path <- file.path(getwd(), "..", "inst", "unitTests")
+     } else {
+       path <- system.file(package=pkg, "unitTests")
+     }
+ 
+     cat("\nRunning unit tests:\n")
+     print(list(pkg=pkg, getwd=getwd(), pathToUnitTests=path))
+     
+     library(package=pkg, character.only=TRUE)
+     
+     # Define tests
+     testSuite <- defineTestSuite(name=paste(pkg, "unit testing"), 
+                                  dirs=path, 
+                                  testFuncRegexp = "^test_+", 
+                                  testFileRegexp = "^test_+")
+     
+     # Run
+     tests <- runTestSuite(testSuite)
+     
+     # Default report name
+     pathReport <- file.path(path, "report")
+     
+     # Report to stdout
+     printTextProtocol(tests, showDetails=FALSE)
+     
+     # Return stop() to cause R CMD check stop in case of
+     #  - failures i.e. FALSE to unit tests or
+     #  - errors i.e. R errors
+     tmp <- getErrors(tests)
+     if(tmp$nFail > 0 | tmp$nErr > 0) {
+       stop(paste("\n\nUnit testing failed (#test failures: ", tmp$nFail, ", 
+                  #R errors: ",  tmp$nErr, ")\n\n", sep=""))
+     }
+     
+   } else {
+     print( "package RUnit not available, cannot run unit tests" )
+   }       
+ }

Running unit tests:
$pkg
[1] "rqt"

$getwd
[1] "C:/Users/biocbuild/bbs-3.9-bioc/meat/rqt.Rcheck/tests_i386"

$pathToUnitTests
[1] "C:/Users/biocbuild/bbs-3.9-bioc/R/library/rqt/unitTests"

Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum



Executing test function test_geneTest  ...  done successfully.



Executing test function test_geneTestMeta  ...  done successfully.

RUNIT TEST PROTOCOL -- Wed Oct 16 06:50:28 2019 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
rqt unit testing - 2 test functions, 0 errors, 0 failures
> 
> proc.time()
   user  system elapsed 
   8.23    0.81    9.20


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.

> # Adapted from: http://rwiki.sciviews.org/doku.php?id=developers:runit
> 
> if( identical( .Platform$OS.type, "windows" ) && 
+     identical( .Platform$r_arch, "x64" ) ){
+   print( "unit tests not run on windows 64 (workaround alert)" )
+ } else {
+   if(require("RUnit", quietly = TRUE)) {
+     pkg <- "rqt"
+     if(Sys.getenv("RCMDCHECK") == "FALSE") {
+       path <- file.path(getwd(), "..", "inst", "unitTests")
+     } else {
+       path <- system.file(package=pkg, "unitTests")
+     }
+ 
+     cat("\nRunning unit tests:\n")
+     print(list(pkg=pkg, getwd=getwd(), pathToUnitTests=path))
+     
+     library(package=pkg, character.only=TRUE)
+     
+     # Define tests
+     testSuite <- defineTestSuite(name=paste(pkg, "unit testing"), 
+                                  dirs=path, 
+                                  testFuncRegexp = "^test_+", 
+                                  testFileRegexp = "^test_+")
+     
+     # Run
+     tests <- runTestSuite(testSuite)
+     
+     # Default report name
+     pathReport <- file.path(path, "report")
+     
+     # Report to stdout
+     printTextProtocol(tests, showDetails=FALSE)
+     
+     # Return stop() to cause R CMD check stop in case of
+     #  - failures i.e. FALSE to unit tests or
+     #  - errors i.e. R errors
+     tmp <- getErrors(tests)
+     if(tmp$nFail > 0 | tmp$nErr > 0) {
+       stop(paste("\n\nUnit testing failed (#test failures: ", tmp$nFail, ", 
+                  #R errors: ",  tmp$nErr, ")\n\n", sep=""))
+     }
+     
+   } else {
+     print( "package RUnit not available, cannot run unit tests" )
+   }       
+ }
[1] "unit tests not run on windows 64 (workaround alert)"
> 
> proc.time()
   user  system elapsed 
   0.20    0.01    0.20

name	user	system	elapsed
rqt-covariates	0.18	0.00	0.40
rqt-geneTest	0.22	0.13	0.35
rqt-geneTestMeta	0.41	0.03	0.99
rqt-genotype	0.03	0.00	0.03
rqt-methods	0.03	0.00	0.03
rqt-phenotype	0.02	0.00	0.02
rqt-results	0.10	0.00	0.11

name	user	system	elapsed
rqt-covariates	0.05	0.04	0.07
rqt-geneTest	0.19	0.00	0.19
rqt-geneTestMeta	0.25	0.00	0.25
rqt-genotype	0.03	0.00	0.03
rqt-methods	0.02	0.00	0.01
rqt-phenotype	0.01	0.01	0.03
rqt-results	0.57	0.00	0.57

CHECK report for rqt on tokay2

Summary

Command output

Installation output

Tests output

Example timings