Multiple platform build/check report for BioC 3.12 - CHECK report for NBSplice on tokay1

Package: NBSplice

Version: 1.8.0

Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NBSplice.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings NBSplice_1.8.0.tar.gz

StartedAt: 2021-05-06 05:01:10 -0400 (Thu, 06 May 2021)

EndedAt: 2021-05-06 05:09:39 -0400 (Thu, 06 May 2021)

EllapsedTime: 509.0 seconds

RetCode: 0

Status: OK

CheckDir: NBSplice.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NBSplice.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings NBSplice_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/NBSplice.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 'NBSplice/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'NBSplice' version '1.8.0'
* 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-NBTest         1.53   0.25   38.78
IsoDataSet-class          1.36   0.39   49.04
IsoDataSet-core           0.94   0.19   35.50
IsoDataSet-buildLowExpIdx 0.35   0.09   15.14
IsoDataSet-constructor    0.31   0.02   10.24
IsoDataSet-initialize     0.18   0.02    9.59
totalGeneCounts           0.14   0.02   10.72
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
IsoDataSet-class          1.20   0.27   48.89
IsoDataSet-NBTest         1.21   0.18   36.62
IsoDataSet-core           0.89   0.19   43.88
IsoDataSet-buildLowExpIdx 0.19   0.12   16.37
totalGeneCounts           0.25   0.00   11.86
IsoDataSet-constructor    0.22   0.01   11.98
IsoDataSet-initialize     0.22   0.00   10.80
* 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://172.29.0.3/BBS/3.12/bioc/src/contrib/NBSplice_1.8.0.tar.gz && rm -rf NBSplice.buildbin-libdir && mkdir NBSplice.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=NBSplice.buildbin-libdir NBSplice_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL NBSplice_1.8.0.zip && rm NBSplice_1.8.0.tar.gz NBSplice_1.8.0.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
  0  918k    0  8517    0     0   378k      0  0:00:02 --:--:--  0:00:02  378k
100  918k  100  918k    0     0  28.2M      0 --:--:-- --:--:-- --:--:-- 28.0M

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_1.8.0.zip
* DONE (NBSplice)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'NBSplice' successfully unpacked and MD5 sums checked


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.

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


RUNIT TEST PROTOCOL -- Thu May 06 05:08:52 2021 
*********************************************** 
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 
  26.10    0.32   26.42


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.

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


RUNIT TEST PROTOCOL -- Thu May 06 05:09:33 2021 
*********************************************** 
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 
  39.76    0.31   40.06

name	user	system	elapsed
IsoDataSet-NBTest	1.53	0.25	38.78
IsoDataSet-buildLowExpIdx	0.35	0.09	15.14
IsoDataSet-class	1.36	0.39	49.04
IsoDataSet-constructor	0.31	0.02	10.24
IsoDataSet-core	0.94	0.19	35.50
IsoDataSet-getters	0.34	0.04	0.39
IsoDataSet-initialize	0.18	0.02	9.59
IsoDataSet-print	0.14	0.00	0.14
IsoDataSet-show	0.22	0.00	0.22
NBSpliceRes-GetDSGenes	0.03	0.00	0.03
NBSpliceRes-GetDSResults	0.02	0.00	0.01
NBSpliceRes-GetGeneResults	0.04	0.00	0.05
NBSpliceRes-class	0.05	0.00	0.05
NBSpliceRes-constructor	0.03	0.00	0.03
NBSpliceRes-getters	0.03	0.00	0.03
NBSpliceRes-initialize	0.04	0.00	0.03
NBSpliceRes-plotGeneResults	0.04	0.00	0.05
NBSpliceRes-plotRatiosDisp	0.03	0.00	0.03
NBSpliceRes-plotVolcano	0.03	0.00	0.03
NBSpliceRes-print	0.04	0.00	0.03
NBSpliceRes-show	0.03	0.00	0.03
totalGeneCounts	0.14	0.02	10.72

name	user	system	elapsed
IsoDataSet-NBTest	1.21	0.18	36.62
IsoDataSet-buildLowExpIdx	0.19	0.12	16.37
IsoDataSet-class	1.20	0.27	48.89
IsoDataSet-constructor	0.22	0.01	11.98
IsoDataSet-core	0.89	0.19	43.88
IsoDataSet-getters	0.36	0.03	0.39
IsoDataSet-initialize	0.22	0.00	10.80
IsoDataSet-print	0.12	0.02	0.14
IsoDataSet-show	0.13	0.01	0.14
NBSpliceRes-GetDSGenes	0.01	0.00	0.01
NBSpliceRes-GetDSResults	0.03	0.00	0.03
NBSpliceRes-GetGeneResults	0.03	0.00	0.03
NBSpliceRes-class	0.04	0.00	0.04
NBSpliceRes-constructor	0.02	0.00	0.02
NBSpliceRes-getters	0.03	0.00	0.03
NBSpliceRes-initialize	0.01	0.00	0.01
NBSpliceRes-plotGeneResults	0.07	0.00	0.06
NBSpliceRes-plotRatiosDisp	0.04	0.00	0.05
NBSpliceRes-plotVolcano	0.03	0.00	0.03
NBSpliceRes-print	0.04	0.00	0.03
NBSpliceRes-show	0.04	0.00	0.05
totalGeneCounts	0.25	0.00	11.86

CHECK report for NBSplice on tokay1

Summary

Command output

Installation output

Tests output

Example timings