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This page was generated on 2022-03-18 11:08:32 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for rqt on riesling1


To the developers/maintainers of the rqt package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rqt.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1662/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rqt 1.21.0  (landing page)
Ilya Y. Zhbannikov
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/rqt
git_branch: master
git_last_commit: db81a01
git_last_commit_date: 2021-10-26 12:33:34 -0400 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  ERROR    ERROR  skippedskipped

Summary

Package: rqt
Version: 1.21.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rqt.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings rqt_1.21.0.tar.gz
StartedAt: 2022-03-17 20:07:41 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 20:09:40 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 118.5 seconds
RetCode: 0
Status:   OK  
CheckDir: rqt.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rqt.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings rqt_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/rqt.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.21.0'
* 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
* 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 ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  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


Installation output

rqt.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL rqt
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* 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
* DONE (rqt)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'sva' is missing or broken
 done

Tests output

rqt.Rcheck/tests/runTests.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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 
   0.21    0.00    0.20 

Example timings

rqt.Rcheck/rqt-Ex.timings

nameusersystemelapsed
rqt-covariates0.060.000.06
rqt-geneTest0.070.010.07
rqt-geneTestMeta0.190.000.19
rqt-genotype0.010.000.01
rqt-methods0.030.000.03
rqt-phenotype0.030.000.03
rqt-results0.100.000.09