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CHECK report for NBSplice on tokay1

This page was generated on 2019-04-13 11:29:31 -0400 (Sat, 13 Apr 2019).

Package 1040/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NBSplice 1.0.6
Gabriela Merino
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/NBSplice
Branch: RELEASE_3_8
Last Commit: d87fa56
Last Changed Date: 2019-04-02 17:03:01 -0400 (Tue, 02 Apr 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: NBSplice
Version: 1.0.6
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NBSplice.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings NBSplice_1.0.6.tar.gz
StartedAt: 2019-04-13 04:07:44 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 04:12:56 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 311.6 seconds
RetCode: 1
Status:  ERROR  
CheckDir: NBSplice.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NBSplice.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings NBSplice_1.0.6.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/NBSplice.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.0.6'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 or elapsed time > 5s
                          user system elapsed
IsoDataSet-class          0.90   0.24   26.34
IsoDataSet-NBTest         0.69   0.20   22.83
IsoDataSet-core           0.71   0.17   22.35
IsoDataSet-buildLowExpIdx 0.23   0.06    6.65
IsoDataSet-initialize     0.11   0.02    5.47
IsoDataSet-constructor    0.12   0.00    6.12
totalGeneCounts           0.02   0.05    5.43
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
IsoDataSet-NBTest         0.77   0.10   21.90
IsoDataSet-class          0.57   0.25   25.52
IsoDataSet-core           0.36   0.13   19.97
IsoDataSet-buildLowExpIdx 0.11   0.06    6.21
totalGeneCounts           0.05   0.01    5.25
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
  1 Test Suite : 
  NBSplice RUnit Tests - 20 test functions, 0 errors, 1 failure
  FAILURE in test_buildLowExpIdx: Error in checkEquals(length(lowExpIndex(aux)), 2224, msg = "buildLowExp length: OK.") : 
    Mean relative difference: 0.02535731
  buildLowExp length: OK.
  
  Test files with failing tests
  
     test_NBSplice.R 
       test_buildLowExpIdx 
  
  
  Error in BiocGenerics:::testPackage("NBSplice") : 
    unit tests failed for package NBSplice
  Execution halted
** 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: 1 ERROR
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/NBSplice.Rcheck/00check.log'
for details.


Installation output

NBSplice.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/NBSplice_1.0.6.tar.gz && rm -rf NBSplice.buildbin-libdir && mkdir NBSplice.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=NBSplice.buildbin-libdir NBSplice_1.0.6.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL NBSplice_1.0.6.zip && rm NBSplice_1.0.6.tar.gz NBSplice_1.0.6.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 1006k  100 1006k    0     0  22.1M      0 --:--:-- --:--:-- --:--:-- 23.9M

install for i386

* installing *source* package 'NBSplice' ...
** 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
In R CMD INSTALL

install for x64

* installing *source* package 'NBSplice' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'NBSplice' as NBSplice_1.0.6.zip
* DONE (NBSplice)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'NBSplice' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

NBSplice.Rcheck/tests_i386/runTests.Rout.fail


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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
Timing stopped at: 0.3 0 0.3
Error in checkEquals(length(lowExpIndex(aux)), 2224, msg = "buildLowExp length: OK.") : 
  Mean relative difference: 0.02535731
buildLowExp length: OK.


RUNIT TEST PROTOCOL -- Sat Apr 13 04:12:46 2019 
*********************************************** 
Number of test functions: 20 
Number of errors: 0 
Number of failures: 1 

 
1 Test Suite : 
NBSplice RUnit Tests - 20 test functions, 0 errors, 1 failure
FAILURE in test_buildLowExpIdx: Error in checkEquals(length(lowExpIndex(aux)), 2224, msg = "buildLowExp length: OK.") : 
  Mean relative difference: 0.02535731
buildLowExp length: OK.

Test files with failing tests

   test_NBSplice.R 
     test_buildLowExpIdx 


Error in BiocGenerics:::testPackage("NBSplice") : 
  unit tests failed for package NBSplice
Execution halted

NBSplice.Rcheck/tests_x64/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 -- Sat Apr 13 04:12:51 2019 
*********************************************** 
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 
   3.98    0.25    4.21 

Example timings

NBSplice.Rcheck/examples_i386/NBSplice-Ex.timings

nameusersystemelapsed
IsoDataSet-NBTest 0.69 0.2022.83
IsoDataSet-buildLowExpIdx0.230.066.65
IsoDataSet-class 0.90 0.2426.34
IsoDataSet-constructor0.120.006.12
IsoDataSet-core 0.71 0.1722.35
IsoDataSet-getters0.510.000.51
IsoDataSet-initialize0.110.025.47
IsoDataSet-print0.220.010.23
IsoDataSet-show0.220.000.22
NBSpliceRes-GetDSGenes0.050.000.08
NBSpliceRes-GetDSResults0.030.000.03
NBSpliceRes-GetGeneResults0.030.000.03
NBSpliceRes-class0.030.020.05
NBSpliceRes-constructor0.030.000.03
NBSpliceRes-getters0.020.010.03
NBSpliceRes-initialize0.010.020.03
NBSpliceRes-plotGeneResults0.10.00.1
NBSpliceRes-plotRatiosDisp0.040.000.05
NBSpliceRes-plotVolcano0.030.000.03
NBSpliceRes-print0.050.000.04
NBSpliceRes-show0.030.000.03
totalGeneCounts0.020.055.43

NBSplice.Rcheck/examples_x64/NBSplice-Ex.timings

nameusersystemelapsed
IsoDataSet-NBTest 0.77 0.1021.90
IsoDataSet-buildLowExpIdx0.110.066.21
IsoDataSet-class 0.57 0.2525.52
IsoDataSet-constructor0.090.004.95
IsoDataSet-core 0.36 0.1319.97
IsoDataSet-getters0.260.010.28
IsoDataSet-initialize0.050.004.73
IsoDataSet-print0.140.000.14
IsoDataSet-show0.120.000.13
NBSpliceRes-GetDSGenes0.020.000.01
NBSpliceRes-GetDSResults0.010.000.02
NBSpliceRes-GetGeneResults0.030.000.03
NBSpliceRes-class0.040.000.03
NBSpliceRes-constructor0.010.000.01
NBSpliceRes-getters0.020.000.02
NBSpliceRes-initialize0.010.000.02
NBSpliceRes-plotGeneResults0.050.000.04
NBSpliceRes-plotRatiosDisp0.030.000.03
NBSpliceRes-plotVolcano0.020.000.02
NBSpliceRes-print0.010.000.01
NBSpliceRes-show0.030.000.03
totalGeneCounts0.050.015.25