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This page was generated on 2016-09-21 03:55:41 -0700 (Wed, 21 Sep 2016).
| Package 124/1257 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| biosigner 1.1.10 Philippe Rinaudo
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | ERROR | ||||||
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK |  | |||||
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ ERROR ] | OK |
| Package: biosigner |
| Version: 1.1.10 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings biosigner_1.1.10.tar.gz |
| StartedAt: 2016-09-20 03:44:38 -0700 (Tue, 20 Sep 2016) |
| EndedAt: 2016-09-20 03:45:45 -0700 (Tue, 20 Sep 2016) |
| EllapsedTime: 67.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: biosigner.Rcheck |
| Warnings: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings biosigner_1.1.10.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/biosigner.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biosigner/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘biosigner’ version ‘1.1.10’
* 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 ‘biosigner’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘Biobase::combine’ by ‘randomForest::combine’ when loading ‘biosigner’
See ‘/Users/biocbuild/bbs-3.4-bioc/meat/biosigner.Rcheck/00install.out’ for details.
* 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 loading without being on the library search path ... 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 ... NOTE
get.REMs: no visible global function definition for ‘extract.bootstrap’
get.REMs: no visible global function definition for
‘get.training.profile.boot’
get.REMs: no visible global function definition for
‘get.training.response.boot’
get.REMs: no visible global function definition for
‘get.test.profile.boot’
get.REMs: no visible global function definition for
‘get.test.response.boot’
get.REMs: no visible global function definition for
‘get.ind.test.profile.boot’
Undefined global functions or variables:
extract.bootstrap get.ind.test.profile.boot get.test.profile.boot
get.test.response.boot get.training.profile.boot
get.training.response.boot
* 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 installed files from ‘inst/doc’ ... 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:
1 Test Suite :
biosigner RUnit Tests - 6 test functions, 1 error, 0 failures
ERROR in test_biosign_plsda: Error in as.vector(target) : could not find function "getSummaryDF"
Test files with failing tests
test_biosigner.R
test_biosign_plsda
Error in BiocGenerics:::testPackage("biosigner") :
unit tests failed for package biosigner
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, 1 WARNING, 1 NOTE
See
‘/Users/biocbuild/bbs-3.4-bioc/meat/biosigner.Rcheck/00check.log’
for details.
runTests.Rout.fail:
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (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("biosigner")
Significant features from 'S' groups:
plsda randomforest svm
m427.215t07.9 "A" "S" "S"
m189.040t01.2 "S" "S" "E"
m995.613t10.2 "E" "S" "A"
m455.221t08.1 "E" "S" "E"
Accuracy:
plsda randomforest svm
Full 0.723 0.714 0.710
AS 0.789 0.757 0.827
S 0.738 0.838 0.696
Significant features from 'S' groups:
plsda
m189.040t01.2 "S"
Accuracy:
plsda
Full 0.723
AS 0.762
S 0.737
dev.new(): using pdf(file="Rplots1.pdf")
dev.new(): using pdf(file="Rplots2.pdf")
dev.new(): using pdf(file="Rplots3.pdf")
dev.new(): using pdf(file="Rplots4.pdf")
dev.new(): using pdf(file="Rplots5.pdf")
Timing stopped at: 0.722 0.042 0.764
Error in as.vector(target) : could not find function "getSummaryDF"
In addition: There were 24 warnings (use warnings() to see them)
Significant features from 'S' groups:
plsda randomforest svm
m427.215t07.9 "A" "S" "B"
m481.313t10.6 "S" "A" "E"
m557.311t10.9 "S" "B" "E"
m497.117t07.7 "S" "E" "E"
m607.308t10.0 "S" "E" "E"
m995.613t10.2 "E" "S" "E"
Accuracy:
plsda randomforest svm
Full 0.633 0.533 0.603
AS 1.000 0.938 0.500
S 0.875 0.857 NA
Significant features from 'S' groups:
randomforest
m189.040t01.2 "S"
m427.215t07.9 "S"
m455.221t08.1 "S"
m995.613t10.2 "S"
Accuracy:
randomforest
Full 0.724
AS 0.800
S 0.747
Significant features from 'S' groups:
plsda randomforest svm
Oxoglutaric acid "S" "S" "S"
Testosterone glucuronide "S" "S" "S"
p-Anisic acid "S" "A" "S"
Pantothenic acid "S" "A" "E"
Acetylphenylalanine "S" "E" "B"
Malic acid "S" "B" "E"
alpha-N-Phenylacetyl-glutamine "S" "E" "E"
Citric acid "S" "E" "E"
Gluconic acid and/or isomers "S" "E" "E"
Glucuronic acid and/or isomers "S" "E" "E"
Hippuric acid "S" "E" "E"
Phe-Tyr-Asp (and isomers) "S" "E" "E"
Threonic acid/Erythronic acid "S" "E" "E"
Accuracy:
plsda randomforest svm
Full 0.896 0.848 0.897
AS 0.874 0.892 0.867
S 0.875 0.848 0.864
dev.new(): using pdf(file="Rplots6.pdf")
No significant variable found for the selected classifier(s): 'svm'
RUNIT TEST PROTOCOL -- Tue Sep 20 03:45:44 2016
***********************************************
Number of test functions: 6
Number of errors: 1
Number of failures: 0
1 Test Suite :
biosigner RUnit Tests - 6 test functions, 1 error, 0 failures
ERROR in test_biosign_plsda: Error in as.vector(target) : could not find function "getSummaryDF"
Test files with failing tests
test_biosigner.R
test_biosign_plsda
Error in BiocGenerics:::testPackage("biosigner") :
unit tests failed for package biosigner
Execution halted
biosigner.Rcheck/00install.out:
* installing *source* package ‘biosigner’ ... ** R ** data ** inst ** preparing package for lazy loading Warning: replacing previous import ‘Biobase::combine’ by ‘randomForest::combine’ when loading ‘biosigner’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded Warning: replacing previous import ‘Biobase::combine’ by ‘randomForest::combine’ when loading ‘biosigner’ * DONE (biosigner)
biosigner.Rcheck/biosigner-Ex.timings:
| name | user | system | elapsed | |
| biosign-class | 2.677 | 0.061 | 2.764 | |
| biosign | 2.570 | 0.052 | 2.623 | |
| biosigner-package | 2.301 | 0.044 | 2.346 | |
| getAccuracyMN | 2.273 | 0.046 | 2.319 | |
| getSignatureLs | 2.345 | 0.052 | 2.397 | |
| plot | 2.586 | 0.044 | 2.632 | |
| predict | 2.580 | 0.041 | 2.624 | |
| show | 2.696 | 0.054 | 2.751 | |