Multiple platform build/check report for BioC 3.14 - CHECK results for NBSplice 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: NBSplice

Version: 1.12.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NBSplice.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings NBSplice_1.12.0.tar.gz

StartedAt: 2022-04-12 23:38:33 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 23:44:51 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 377.4 seconds

RetCode: 0

Status: OK

CheckDir: NBSplice.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:NBSplice.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings NBSplice_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/NBSplice.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 'NBSplice/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'NBSplice' version '1.12.0'
* 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 'NBSplice' 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
IsoDataSet-class          1.45   0.39   38.25
IsoDataSet-NBTest         1.56   0.26   29.71
IsoDataSet-core           1.29   0.21   28.70
IsoDataSet-buildLowExpIdx 0.42   0.07    9.17
IsoDataSet-constructor    0.24   0.04    8.62
IsoDataSet-initialize     0.25   0.02    8.34
totalGeneCounts           0.17   0.05    9.12
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
IsoDataSet-NBTest         1.60   0.29   31.41
IsoDataSet-class          1.54   0.30   39.80
IsoDataSet-core           1.42   0.19   30.61
IsoDataSet-buildLowExpIdx 0.39   0.13    9.90
IsoDataSet-constructor    0.29   0.01    8.90
IsoDataSet-initialize     0.27   0.02    8.78
totalGeneCounts           0.19   0.03    8.79
* 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 http://155.52.207.166/BBS/3.14/bioc/src/contrib/NBSplice_1.12.0.tar.gz && rm -rf NBSplice.buildbin-libdir && mkdir NBSplice.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=NBSplice.buildbin-libdir NBSplice_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL NBSplice_1.12.0.zip && rm NBSplice_1.12.0.tar.gz NBSplice_1.12.0.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  917k  100  917k    0     0  1215k      0 --:--:-- --:--:-- --:--:-- 1217k

install for i386

* installing *source* package 'NBSplice' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'NBSplice'
    finding HTML links ... done
    IsoDataSet-NBTest                       html  
    IsoDataSet-buildLowExpIdx               html  
    IsoDataSet-class                        html  
    IsoDataSet-constructor                  html  
    IsoDataSet-core                         html  
    IsoDataSet-getters                      html  
    IsoDataSet-initialize                   html  
    IsoDataSet-print                        html  
    IsoDataSet-show                         html  
    NBSplice-package                        html  
    NBSpliceRes-GetDSGenes                  html  
    NBSpliceRes-GetDSResults                html  
    NBSpliceRes-GetGeneResults              html  
    NBSpliceRes-class                       html  
    NBSpliceRes-constructor                 html  
    NBSpliceRes-getters                     html  
    NBSpliceRes-initialize                  html  
    NBSpliceRes-plotGeneResults             html  
    NBSpliceRes-plotRatiosDisp              html  
    NBSpliceRes-plotVolcano                 html  
    NBSpliceRes-print                       html  
    NBSpliceRes-show                        html  
    designMatrix                            html  
    geneIso                                 html  
    isoCountsData                           html  
    myDSResults                             html  
    myIsoDataSet                            html  
    totalGeneCounts                         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 'NBSplice' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'NBSplice' as NBSplice_1.12.0.zip
* DONE (NBSplice)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'NBSplice' 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.

> BiocGenerics:::testPackage("NBSplice")
Loading required package: BiocParallel
Loading required package: ggplot2


RUNIT TEST PROTOCOL -- Tue Apr 12 23:44:36 2022 
*********************************************** 
Number of test functions: 20 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
NBSplice RUnit Tests - 20 test functions, 0 errors, 0 failures
Number of test functions: 20 
Number of errors: 0 
Number of failures: 0 
> 
> 
> proc.time()
   user  system elapsed 
   4.48    0.17    4.64


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.

> BiocGenerics:::testPackage("NBSplice")
Loading required package: BiocParallel
Loading required package: ggplot2


RUNIT TEST PROTOCOL -- Tue Apr 12 23:44:42 2022 
*********************************************** 
Number of test functions: 20 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
NBSplice RUnit Tests - 20 test functions, 0 errors, 0 failures
Number of test functions: 20 
Number of errors: 0 
Number of failures: 0 
> 
> 
> proc.time()
   user  system elapsed 
   4.81    0.18    4.98

name	user	system	elapsed
IsoDataSet-NBTest	1.56	0.26	29.71
IsoDataSet-buildLowExpIdx	0.42	0.07	9.17
IsoDataSet-class	1.45	0.39	38.25
IsoDataSet-constructor	0.24	0.04	8.62
IsoDataSet-core	1.29	0.21	28.70
IsoDataSet-getters	0.44	0.01	0.46
IsoDataSet-initialize	0.25	0.02	8.34
IsoDataSet-print	0.24	0.00	0.24
IsoDataSet-show	0.18	0.00	0.18
NBSpliceRes-GetDSGenes	0.03	0.00	0.03
NBSpliceRes-GetDSResults	0.04	0.00	0.04
NBSpliceRes-GetGeneResults	0.03	0.01	0.04
NBSpliceRes-class	0.03	0.00	0.03
NBSpliceRes-constructor	0.03	0.00	0.03
NBSpliceRes-getters	0.03	0.00	0.04
NBSpliceRes-initialize	0.02	0.00	0.01
NBSpliceRes-plotGeneResults	0.06	0.00	0.06
NBSpliceRes-plotRatiosDisp	0.03	0.00	0.04
NBSpliceRes-plotVolcano	0.03	0.00	0.03
NBSpliceRes-print	0.02	0.02	0.03
NBSpliceRes-show	0.03	0.00	0.03
totalGeneCounts	0.17	0.05	9.12

name	user	system	elapsed
IsoDataSet-NBTest	1.60	0.29	31.41
IsoDataSet-buildLowExpIdx	0.39	0.13	9.90
IsoDataSet-class	1.54	0.30	39.80
IsoDataSet-constructor	0.29	0.01	8.90
IsoDataSet-core	1.42	0.19	30.61
IsoDataSet-getters	0.45	0.00	0.45
IsoDataSet-initialize	0.27	0.02	8.78
IsoDataSet-print	0.22	0.03	0.25
IsoDataSet-show	0.17	0.02	0.18
NBSpliceRes-GetDSGenes	0.01	0.00	0.02
NBSpliceRes-GetDSResults	0.04	0.00	0.03
NBSpliceRes-GetGeneResults	0.03	0.00	0.03
NBSpliceRes-class	0.03	0.00	0.03
NBSpliceRes-constructor	0.03	0.00	0.03
NBSpliceRes-getters	0.02	0.00	0.02
NBSpliceRes-initialize	0.01	0.00	0.02
NBSpliceRes-plotGeneResults	0.06	0.00	0.06
NBSpliceRes-plotRatiosDisp	0.03	0.00	0.03
NBSpliceRes-plotVolcano	0.04	0.00	0.03
NBSpliceRes-print	0.01	0.00	0.02
NBSpliceRes-show	0.03	0.00	0.03
totalGeneCounts	0.19	0.03	8.79

CHECK results for NBSplice on tokay2

Summary

Command output

Installation output

Tests output

Example timings