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) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:29:31 -0400 (Sat, 13 Apr 2019).
| Package 1040/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| NBSplice 1.0.6 Gabriela Merino
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| 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 | |
| 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 |
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### Running command:
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### 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.
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
|
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
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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
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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
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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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