| Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 13:15:44 -0400 (Tue, 09 Apr 2019).
| Package 1093/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| nucleoSim 1.11.0 Astrid Deschenes
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ ERROR ] | OK | |||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: nucleoSim |
| Version: 1.11.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:nucleoSim.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings nucleoSim_1.11.0.tar.gz |
| StartedAt: 2019-04-09 04:00:30 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 04:01:59 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 88.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: nucleoSim.Rcheck |
| Warnings: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:nucleoSim.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings nucleoSim_1.11.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/nucleoSim.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘nucleoSim/DESCRIPTION’ ... OK
* this is package ‘nucleoSim’ version ‘1.11.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘nucleoSim’ 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
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
test.syntheticNucMapFromDist_good_result_01
test.syntheticNucMapFromDist_good_result_02
test.syntheticNucMapFromDist_good_result_03
test.syntheticNucMapFromDist_good_result_04
test_syntheticNucReadsFromMap.R
test.syntheticNucReadsFromMap_good_result_01
test_syntheticSampleFromDist.R
test.syntheticNucReadsFromDist_good_result_02
Error in BiocGenerics:::testPackage("nucleoSim") :
unit tests failed for package nucleoSim
Execution halted
* 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
‘/Users/biocbuild/bbs-3.9-bioc/meat/nucleoSim.Rcheck/00check.log’
for details.
nucleoSim.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL nucleoSim ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘nucleoSim’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * DONE (nucleoSim)
nucleoSim.Rcheck/tests/runTests.Rout.fail
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
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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
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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.
> ## Run all tests present in the package
> BiocGenerics:::testPackage("nucleoSim")
Timing stopped at: 0.082 0.021 0.103
Error in checkEqualsNumeric(obs$wp.starts, exp.wp.starts, msg = message) :
Mean relative difference: 0.4983498
test.syntheticNucMapFromDist_good_result_01() - syntheticNucMapFromDist did not generated expected values
Timing stopped at: 0.006 0.001 0.006
Error in checkEqualsNumeric(obs$wp.starts, exp.wp.starts, msg = message) :
Mean relative difference: 0.6637363
test.syntheticNucMapFromDist_good_result_02() - syntheticNucMapFromDist did not generated expected values
Timing stopped at: 0.005 0.001 0.006
Error in checkEqualsNumeric(obs$fuz.starts, exp.fuz.starts, msg = message) :
Mean relative difference: 1.342365
test.syntheticNucMapFromDist_good_result_03() - syntheticNucMapFromDist did not generated expected values
Timing stopped at: 0.009 0.002 0.011
Error in checkEqualsNumeric(obs$wp.starts, exp.wp.starts, msg = message) :
Mean relative difference: 0.3325991
test.syntheticNucMapFromDist_good_result_04() - syntheticNucMapFromDist did not generated expected values
Timing stopped at: 0.049 0.007 0.057
Error in checkEqualsNumeric(obs$wp, exp.wp, msg = message) :
Mean relative difference: 0.1494624
test.syntheticNucReadsFromMap_good_result_01() - syntheticNucReadsFromMap did not generate expected values
Timing stopped at: 0.014 0 0.014
Error in checkEqualsNumeric(obs$wp, exp.wp, msg = message) :
Mean relative difference: 0.275069
test.syntheticNucReadsFromDist_good_result_02() - syntheticNucReadsFromDist did not generate expected values
RUNIT TEST PROTOCOL -- Tue Apr 9 04:01:52 2019
***********************************************
Number of test functions: 74
Number of errors: 0
Number of failures: 6
1 Test Suite :
nucleoSim RUnit Tests - 74 test functions, 0 errors, 6 failures
FAILURE in test.syntheticNucMapFromDist_good_result_01: Error in checkEqualsNumeric(obs$wp.starts, exp.wp.starts, msg = message) :
Mean relative difference: 0.4983498
test.syntheticNucMapFromDist_good_result_01() - syntheticNucMapFromDist did not generated expected values
FAILURE in test.syntheticNucMapFromDist_good_result_02: Error in checkEqualsNumeric(obs$wp.starts, exp.wp.starts, msg = message) :
Mean relative difference: 0.6637363
test.syntheticNucMapFromDist_good_result_02() - syntheticNucMapFromDist did not generated expected values
FAILURE in test.syntheticNucMapFromDist_good_result_03: Error in checkEqualsNumeric(obs$fuz.starts, exp.fuz.starts, msg = message) :
Mean relative difference: 1.342365
test.syntheticNucMapFromDist_good_result_03() - syntheticNucMapFromDist did not generated expected values
FAILURE in test.syntheticNucMapFromDist_good_result_04: Error in checkEqualsNumeric(obs$wp.starts, exp.wp.starts, msg = message) :
Mean relative difference: 0.3325991
test.syntheticNucMapFromDist_good_result_04() - syntheticNucMapFromDist did not generated expected values
FAILURE in test.syntheticNucReadsFromMap_good_result_01: Error in checkEqualsNumeric(obs$wp, exp.wp, msg = message) :
Mean relative difference: 0.1494624
test.syntheticNucReadsFromMap_good_result_01() - syntheticNucReadsFromMap did not generate expected values
FAILURE in test.syntheticNucReadsFromDist_good_result_02: Error in checkEqualsNumeric(obs$wp, exp.wp, msg = message) :
Mean relative difference: 0.275069
test.syntheticNucReadsFromDist_good_result_02() - syntheticNucReadsFromDist did not generate expected values
Test files with failing tests
test_syntheticNucMapFromDist.R
test.syntheticNucMapFromDist_good_result_01
test.syntheticNucMapFromDist_good_result_02
test.syntheticNucMapFromDist_good_result_03
test.syntheticNucMapFromDist_good_result_04
test_syntheticNucReadsFromMap.R
test.syntheticNucReadsFromMap_good_result_01
test_syntheticSampleFromDist.R
test.syntheticNucReadsFromDist_good_result_02
Error in BiocGenerics:::testPackage("nucleoSim") :
unit tests failed for package nucleoSim
Execution halted
nucleoSim.Rcheck/nucleoSim-Ex.timings
| name | user | system | elapsed | |
| createNucReadsFromNucMap | 0.064 | 0.014 | 0.079 | |
| plot.syntheticNucMap | 0.033 | 0.008 | 0.041 | |
| plot.syntheticNucReads | 0.048 | 0.003 | 0.052 | |
| syntheticNucMapFromDist | 0.077 | 0.007 | 0.084 | |
| syntheticNucMapFromDistValidation | 0.001 | 0.001 | 0.001 | |
| syntheticNucReadsFromDist | 0.017 | 0.002 | 0.019 | |
| syntheticNucReadsFromMap | 0.017 | 0.001 | 0.018 | |
| syntheticNucReadsValidation | 0.001 | 0.000 | 0.001 | |