Multiple platform build/check report for BioC 3.14 - CHECK results for MOGAMUN on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
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*

Package: MOGAMUN

Version: 1.4.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MOGAMUN.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MOGAMUN_1.4.0.tar.gz

StartedAt: 2022-04-12 23:08:20 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 23:09:46 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 86.5 seconds

RetCode: 0

Status: OK

CheckDir: MOGAMUN.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MOGAMUN.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MOGAMUN_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MOGAMUN.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.4.0'
* 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 '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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/MOGAMUN_1.4.0.tar.gz && rm -rf MOGAMUN.buildbin-libdir && mkdir MOGAMUN.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MOGAMUN.buildbin-libdir MOGAMUN_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL MOGAMUN_1.4.0.zip && rm MOGAMUN_1.4.0.tar.gz MOGAMUN_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  114k  100  114k    0     0   593k      0 --:--:-- --:--:-- --:--:--  597k

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_1.4.0.zip
* DONE (MOGAMUN)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'MOGAMUN' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 -- Tue Apr 12 23:09:35 2022 
*********************************************** 
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-3.14-bioc/R/library/MOGAMUN/tests/test.mogamun.R 
no test files 
> 
> 
> proc.time()
   user  system elapsed 
   1.98    0.12    2.09


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 -- Tue Apr 12 23:09:37 2022 
*********************************************** 
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-3.14-bioc/R/library/MOGAMUN/tests/test.mogamun.R 
no test files 
> 
> 
> proc.time()
   user  system elapsed 
   2.03    0.14    2.17

name	user	system	elapsed
mogamun_init	0	0	0
mogamun_load_data	0.05	0.02	0.11
mogamun_postprocess	1.16	0.03	1.19
mogamun_run	0.73	0.01	0.75

name	user	system	elapsed
mogamun_init	0	0	0
mogamun_load_data	0.03	0.00	0.04
mogamun_postprocess	1.12	0.04	1.27
mogamun_run	0.94	0.03	0.97

CHECK results for MOGAMUN on tokay2

Summary

Command output

Installation output

Tests output

Example timings