Back to Multiple platform build/check report for BioC 3.12
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

CHECK report for MOGAMUN on tokay1

This page was generated on 2021-05-06 12:32:19 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the MOGAMUN package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1135/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MOGAMUN 1.0.1  (landing page)
Elva-MarĂ­a Novoa-del-Toro
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/MOGAMUN
Branch: RELEASE_3_12
Last Commit: a65e3fb
Last Changed Date: 2021-02-12 09:58:06 -0400 (Fri, 12 Feb 2021)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: MOGAMUN
Version: 1.0.1
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MOGAMUN.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MOGAMUN_1.0.1.tar.gz
StartedAt: 2021-05-06 04:46:56 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:48:04 -0400 (Thu, 06 May 2021)
EllapsedTime: 68.1 seconds
RetCode: 0
Status:   OK   
CheckDir: MOGAMUN.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MOGAMUN.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MOGAMUN_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/MOGAMUN.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MOGAMUN/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MOGAMUN' version '1.0.1'
* 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 'MOGAMUN' 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
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'unitTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'unitTests.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

MOGAMUN.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/MOGAMUN_1.0.1.tar.gz && rm -rf MOGAMUN.buildbin-libdir && mkdir MOGAMUN.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MOGAMUN.buildbin-libdir MOGAMUN_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL MOGAMUN_1.0.1.zip && rm MOGAMUN_1.0.1.tar.gz MOGAMUN_1.0.1.zip
###
##############################################################################
##############################################################################


  % 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 98732  100 98732    0     0  5186k      0 --:--:-- --:--:-- --:--:-- 5356k

install for i386

* installing *source* package 'MOGAMUN' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MOGAMUN'
    finding HTML links ... done
    mogamun_init                            html  
    mogamun_load_data                       html  
    mogamun_postprocess                     html  
    mogamun_run                             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 'MOGAMUN' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MOGAMUN' as MOGAMUN_1.0.1.zip
* DONE (MOGAMUN)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'MOGAMUN' successfully unpacked and MD5 sums checked

Tests output

MOGAMUN.Rcheck/tests_i386/unitTests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.

> # Our package. Used for the test suite name
> pkgname <- c("MOGAMUN", "RUnit")
> 
> for (p in pkgname) {
+     require(p, quietly=TRUE, character.only=TRUE) || 
+     stop("package '", p, "' not found")
+ }
> 
> pkgname <- "MOGAMUN"
> 
> # Determine which files to load (have to start with test_ and end with .R)
> pattern <- "^test.*\\.R$"
> 
> # Which functions to run. Have to start with 'test.'
> testFunctionRegexp = "^test.+"
> 
> # Path to the unit tests folder in the package
> directory <- paste0(system.file("tests", package=pkgname), "/")
> if (.Platform$OS.type == "windows") { # windows needs the absolute file names
+     directory <- list.files(directory, pattern = pattern, full.names = TRUE)
+ } 
> 
> for (dir in directory) {
+     # Define RUnit test suite
+     suite <- defineTestSuite(name=paste(pkgname, "RUnit Tests"),
+                              dirs=dir,
+                              testFileRegexp=pattern,
+                              testFuncRegexp = testFunctionRegexp,
+                              rngKind="default",
+                              rngNormalKind="default")
+     
+     # Run tests
+     result <- runTestSuite(suite)
+     
+     # Display result tests on the console
+     printTextProtocol(result)
+     
+     # Write results in JUnit-like xml format
+     printJUnitProtocol(result, fileName="junit.xml")
+ }
RUNIT TEST PROTOCOL -- Thu May 06 04:47:58 2021 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
MOGAMUN RUnit Tests - 0 test functions, 0 errors, 0 failures



Details 
*************************** 
Test Suite: MOGAMUN RUnit Tests 
Test function regexp: ^test.+ 
Test file regexp: ^test.*\.R$ 
Involved directory: 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/MOGAMUN/tests/test.mogamun.R 
no test files 
> 
> 
> proc.time()
   user  system elapsed 
   1.76    0.18    1.96 

MOGAMUN.Rcheck/tests_x64/unitTests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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.

> # Our package. Used for the test suite name
> pkgname <- c("MOGAMUN", "RUnit")
> 
> for (p in pkgname) {
+     require(p, quietly=TRUE, character.only=TRUE) || 
+     stop("package '", p, "' not found")
+ }
> 
> pkgname <- "MOGAMUN"
> 
> # Determine which files to load (have to start with test_ and end with .R)
> pattern <- "^test.*\\.R$"
> 
> # Which functions to run. Have to start with 'test.'
> testFunctionRegexp = "^test.+"
> 
> # Path to the unit tests folder in the package
> directory <- paste0(system.file("tests", package=pkgname), "/")
> if (.Platform$OS.type == "windows") { # windows needs the absolute file names
+     directory <- list.files(directory, pattern = pattern, full.names = TRUE)
+ } 
> 
> for (dir in directory) {
+     # Define RUnit test suite
+     suite <- defineTestSuite(name=paste(pkgname, "RUnit Tests"),
+                              dirs=dir,
+                              testFileRegexp=pattern,
+                              testFuncRegexp = testFunctionRegexp,
+                              rngKind="default",
+                              rngNormalKind="default")
+     
+     # Run tests
+     result <- runTestSuite(suite)
+     
+     # Display result tests on the console
+     printTextProtocol(result)
+     
+     # Write results in JUnit-like xml format
+     printJUnitProtocol(result, fileName="junit.xml")
+ }
RUNIT TEST PROTOCOL -- Thu May 06 04:48:01 2021 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
MOGAMUN RUnit Tests - 0 test functions, 0 errors, 0 failures



Details 
*************************** 
Test Suite: MOGAMUN RUnit Tests 
Test function regexp: ^test.+ 
Test file regexp: ^test.*\.R$ 
Involved directory: 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/MOGAMUN/tests/test.mogamun.R 
no test files 
> 
> 
> proc.time()
   user  system elapsed 
   1.64    0.10    1.96 

Example timings

MOGAMUN.Rcheck/examples_i386/MOGAMUN-Ex.timings

nameusersystemelapsed
mogamun_init000
mogamun_load_data0.050.000.05
mogamun_postprocess1.500.081.75
mogamun_run1.750.031.80

MOGAMUN.Rcheck/examples_x64/MOGAMUN-Ex.timings

nameusersystemelapsed
mogamun_init000
mogamun_load_data0.030.000.03
mogamun_postprocess1.970.011.98
mogamun_run1.30.01.3