Gabriela Merino
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/NBSplice |
| Branch: master |
| Last Commit: 4188f56 |
| Last Changed Date: 2019-03-25 14:27:39 -0400 (Mon, 25 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:40:58 -0400 (Tue, 09 Apr 2019).
| Package 1067/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| NBSplice 1.1.7 Gabriela Merino
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
| Package: NBSplice |
| Version: 1.1.7 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NBSplice.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings NBSplice_1.1.7.tar.gz |
| StartedAt: 2019-04-09 04:31:38 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 04:37:03 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 325.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: NBSplice.Rcheck |
| Warnings: NA |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NBSplice.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings NBSplice_1.1.7.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/NBSplice.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '1.1.7'
* 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 or elapsed time > 5s
user system elapsed
IsoDataSet-NBTest 0.99 0.14 27.24
IsoDataSet-class 0.93 0.17 35.72
IsoDataSet-core 0.72 0.14 24.78
IsoDataSet-buildLowExpIdx 0.15 0.07 7.62
IsoDataSet-constructor 0.08 0.06 12.13
IsoDataSet-initialize 0.10 0.01 6.68
totalGeneCounts 0.04 0.03 6.10
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
IsoDataSet-class 0.92 0.20 35.46
IsoDataSet-NBTest 0.88 0.22 25.48
IsoDataSet-core 0.69 0.12 25.69
IsoDataSet-buildLowExpIdx 0.17 0.10 8.16
IsoDataSet-constructor 0.09 0.00 6.96
IsoDataSet-initialize 0.07 0.00 7.31
totalGeneCounts 0.05 0.00 6.97
* 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 checkEqualsNumeric(round(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-3.9-bioc/meat/NBSplice.Rcheck/00check.log'
for details.
NBSplice.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/NBSplice_1.1.7.tar.gz && rm -rf NBSplice.buildbin-libdir && mkdir NBSplice.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=NBSplice.buildbin-libdir NBSplice_1.1.7.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL NBSplice_1.1.7.zip && rm NBSplice_1.1.7.tar.gz NBSplice_1.1.7.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 916k 100 916k 0 0 13.8M 0 --:--:-- --:--:-- --:--:-- 15.4M
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 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_1.1.7.zip
* DONE (NBSplice)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'NBSplice' successfully unpacked and MD5 sums checked
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NBSplice.Rcheck/tests_i386/runTests.Rout.fail
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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: 0.38 0 0.37
Error in checkEqualsNumeric(round(length(lowExpIndex(aux))), 2224, msg = "buildLowExp length: OK.") :
Mean relative difference: 0.02535731
buildLowExp length: OK.
RUNIT TEST PROTOCOL -- Tue Apr 09 04:36:50 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 checkEqualsNumeric(round(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
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NBSplice.Rcheck/tests_x64/runTests.Rout
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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 -- Tue Apr 09 04:36:54 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
4.25 0.23 4.48
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NBSplice.Rcheck/examples_i386/NBSplice-Ex.timings
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NBSplice.Rcheck/examples_x64/NBSplice-Ex.timings
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