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This page was generated on 2021-10-21 12:04:56 -0400 (Thu, 21 Oct 2021).

CHECK results for NBSplice on riesling1

To the developers/maintainers of the NBSplice package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NBSplice.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 1267/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NBSplice 1.11.2  (landing page)
Gabriela Merino
Snapshot Date: 2021-10-20 14:50:05 -0400 (Wed, 20 Oct 2021)
git_url: https://git.bioconductor.org/packages/NBSplice
git_branch: master
git_last_commit: ba4d4ee
git_last_commit_date: 2021-09-03 10:24:59 -0400 (Fri, 03 Sep 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    NA  

Summary

Package: NBSplice
Version: 1.11.2
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NBSplice.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings NBSplice_1.11.2.tar.gz
StartedAt: 2021-10-21 02:54:01 -0400 (Thu, 21 Oct 2021)
EndedAt: 2021-10-21 02:58:20 -0400 (Thu, 21 Oct 2021)
EllapsedTime: 259.1 seconds
RetCode: 0
Status:   OK  
CheckDir: NBSplice.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NBSplice.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings NBSplice_1.11.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/NBSplice.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.11.2'
* 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          0.69   0.22   23.15
IsoDataSet-NBTest         0.68   0.12   17.33
IsoDataSet-core           0.59   0.08   17.22
IsoDataSet-buildLowExpIdx 0.22   0.03    5.58
IsoDataSet-initialize     0.14   0.02    5.53
totalGeneCounts           0.11   0.05    5.27
IsoDataSet-constructor    0.10   0.03    5.46
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
IsoDataSet-NBTest         0.66   0.02   17.60
IsoDataSet-class          0.58   0.06   22.81
IsoDataSet-core           0.51   0.08   17.41
IsoDataSet-buildLowExpIdx 0.22   0.00    5.63
IsoDataSet-initialize     0.17   0.01    5.50
IsoDataSet-constructor    0.17   0.00    5.64
totalGeneCounts           0.15   0.00    5.45
* 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


Installation output

NBSplice.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/NBSplice_1.11.2.tar.gz && rm -rf NBSplice.buildbin-libdir && mkdir NBSplice.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=NBSplice.buildbin-libdir NBSplice_1.11.2.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL NBSplice_1.11.2.zip && rm NBSplice_1.11.2.tar.gz NBSplice_1.11.2.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  917k  100  917k    0     0  2684k      0 --:--:-- --:--:-- --:--:-- 2684k

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_1.11.2.zip
* DONE (NBSplice)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'NBSplice' successfully unpacked and MD5 sums checked

Tests output

NBSplice.Rcheck/tests_i386/runTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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 Oct 21 02:57:31 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 
   2.85    0.18    3.03 

NBSplice.Rcheck/tests_x64/runTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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 Oct 21 02:57:34 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 
   2.89    0.18    3.06 

Example timings

NBSplice.Rcheck/examples_i386/NBSplice-Ex.timings

nameusersystemelapsed
IsoDataSet-NBTest 0.68 0.1217.33
IsoDataSet-buildLowExpIdx0.220.035.58
IsoDataSet-class 0.69 0.2223.15
IsoDataSet-constructor0.100.035.46
IsoDataSet-core 0.59 0.0817.22
IsoDataSet-getters0.220.030.25
IsoDataSet-initialize0.140.025.53
IsoDataSet-print0.080.000.08
IsoDataSet-show0.080.000.08
NBSpliceRes-GetDSGenes0.020.000.01
NBSpliceRes-GetDSResults0.010.000.02
NBSpliceRes-GetGeneResults0.020.000.01
NBSpliceRes-class0.030.000.03
NBSpliceRes-constructor0.010.000.02
NBSpliceRes-getters0.020.000.02
NBSpliceRes-initialize0.010.000.01
NBSpliceRes-plotGeneResults0.020.010.03
NBSpliceRes-plotRatiosDisp0.020.000.02
NBSpliceRes-plotVolcano0.010.000.01
NBSpliceRes-print0.020.020.03
NBSpliceRes-show0.010.000.02
totalGeneCounts0.110.055.27

NBSplice.Rcheck/examples_x64/NBSplice-Ex.timings

nameusersystemelapsed
IsoDataSet-NBTest 0.66 0.0217.60
IsoDataSet-buildLowExpIdx0.220.005.63
IsoDataSet-class 0.58 0.0622.81
IsoDataSet-constructor0.170.005.64
IsoDataSet-core 0.51 0.0817.41
IsoDataSet-getters0.190.020.20
IsoDataSet-initialize0.170.015.50
IsoDataSet-print0.070.000.07
IsoDataSet-show0.070.000.07
NBSpliceRes-GetDSGenes0.020.000.02
NBSpliceRes-GetDSResults0.020.000.02
NBSpliceRes-GetGeneResults0.010.000.01
NBSpliceRes-class0.020.000.02
NBSpliceRes-constructor0.010.000.01
NBSpliceRes-getters0.020.000.02
NBSpliceRes-initialize0.010.000.01
NBSpliceRes-plotGeneResults0.030.000.03
NBSpliceRes-plotRatiosDisp0.020.000.02
NBSpliceRes-plotVolcano0.020.000.02
NBSpliceRes-print0.010.000.01
NBSpliceRes-show0.020.000.02
totalGeneCounts0.150.005.45