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BioC 3.3: CHECK report for LedPred on morelia

This page was generated on 2016-04-21 13:26:53 -0700 (Thu, 21 Apr 2016).

Package 624/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LedPred 1.5.0
Aitor Gonzalez
Snapshot Date: 2016-04-20 17:20:35 -0700 (Wed, 20 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/LedPred
Last Changed Rev: 116543 / Revision: 116626
Last Changed Date: 2016-04-19 04:16:28 -0700 (Tue, 19 Apr 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  ERROR 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  ERROR  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ ERROR ] OK 

Summary

Package: LedPred
Version: 1.5.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LedPred_1.5.0.tar.gz
StartedAt: 2016-04-21 04:22:16 -0700 (Thu, 21 Apr 2016)
EndedAt: 2016-04-21 04:23:09 -0700 (Thu, 21 Apr 2016)
EllapsedTime: 52.6 seconds
RetCode: 1
Status:  ERROR 
CheckDir: LedPred.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LedPred_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/LedPred.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LedPred/DESCRIPTION’ ... OK
* this is package ‘LedPred’ version ‘1.5.0’
* 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 ‘LedPred’ can be installed ... [2s/12s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
  MIT
* 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
.plotCostGamma: no visible global function definition for ‘title’
.plotCostGamma: no visible global function definition for ‘points’
mapFeaturesToCRMs: no visible global function definition for
  ‘write.table’
mapFeaturesToCRMs: no visible global function definition for
  ‘read.table’
mapFeaturesToCRMs: no visible global function definition for
  ‘download.file’
scoreData: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  download.file points read.table title write.table
Consider adding
  importFrom("graphics", "points", "title")
  importFrom("utils", "download.file", "read.table", "write.table")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [1s/1s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [22s/9s]
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1. Error: create_model (data.frame) (@test-createModel.r#14) 
  2. Error: create_model (genomic.ranges) (@test-createModel.r#24) 
  3. Error: evaluate_model_performance (data.frame) (@test-evaluateModelPerformance.r#15) 
  4. Error: evaluate_model_performance (data.frame) (@test-evaluateModelPerformance.r#24) 
  5. Error: Tune cost gamma (crm.features.tab) (@test-mcTune.r#15) 
  6. Error: Tune cost gamma (crm.features.granges) (@test-mcTune.r#26) 
  7. Error: Rank features (df) (@test-rankFeatures.r#12) 
  8. Error: Rank features (seq.ranges) (@test-rankFeatures.r#22) 
  9. Error: scoreData (data.frame) (@test-scoreData.r#7) 
  1. ...
  
  Error: testthat unit tests failed
  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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/LedPred.Rcheck/00check.log’
for details.

testthat.Rout.fail:


R version 3.3.0 beta (2016-04-06 r70435) -- "Supposedly Educational"
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.

> library(testthat)
> library(LedPred)
Loading required package: e1071
> 
> test_check("LedPred")
1. Error: create_model (data.frame) (@test-createModel.r#14) -------------------
unused argument (scale = scale)
1: createModel(data = feature.matrix, cl = cl, kernel = kernel, scale = scale, cost = cost, 
       gamma = gamma, feature.rank = feature.ranking, feature.nb = feature.nb) at testthat/test-createModel.r:14

2. Error: create_model (genomic.ranges) (@test-createModel.r#24) ---------------
unused arguments (data.granges = crm.features, scale = scale)
1: createModel(data.granges = crm.features, cl = cl, kernel = kernel, scale = scale, 
       cost = cost, gamma = gamma, feature.rank = feature.ranking, feature.nb = feature.nb) at testthat/test-createModel.r:24

3. Error: evaluate_model_performance (data.frame) (@test-evaluateModelPerformance.r#15) 
unused argument (scale = scale)
1: evaluateModelPerformance(data = feature.matrix, cl = 1, valid.times = valid.times, 
       feature.rank = feature.ranking, feature.nb = feature.nb, kernel = kernel, scale = scale, 
       cost = cost, gamma = gamma) at testthat/test-evaluateModelPerformance.r:15

4. Error: evaluate_model_performance (data.frame) (@test-evaluateModelPerformance.r#24) 
unused arguments (data.granges = crm.features, scale = scale)
1: evaluateModelPerformance(data.granges = crm.features, cl = 1, valid.times = valid.times, 
       feature.rank = feature.ranking, feature.nb = feature.nb, kernel = kernel, scale = scale, 
       cost = cost, gamma = gamma) at testthat/test-evaluateModelPerformance.r:24

5. Error: Tune cost gamma (crm.features.tab) (@test-mcTune.r#15) ---------------
unused argument (scale = scale)
1: mcTune(data = feature.matrix, cl = 1, ranges = list(gamma = gamma_vector, cost = cost_vector), 
       kernel = kernel, scale = scale, valid.times = valid.times) at testthat/test-mcTune.r:15

6. Error: Tune cost gamma (crm.features.granges) (@test-mcTune.r#26) -----------
unused arguments (data.granges = crm.features, scale = scale)
1: mcTune(data.granges = crm.features, cl = 1, ranges = list(gamma = gamma_vector, cost = cost_vector), 
       kernel = kernel, scale = scale, valid.times = valid.times) at testthat/test-mcTune.r:26

7. Error: Rank features (df) (@test-rankFeatures.r#12) -------------------------
unused argument (scale = scale)
1: rankFeatures(data = feature.matrix, halve.above = 100, valid.times = valid.times, 
       kernel = kernel, cost = cost, gamma = gamma, scale = scale) at testthat/test-rankFeatures.r:12

8. Error: Rank features (seq.ranges) (@test-rankFeatures.r#22) -----------------
unused arguments (data.granges = crm.features, scale = scale)
1: rankFeatures(data.granges = crm.features, halve.above = 100, valid.times = valid.times, 
       kernel = kernel, cost = cost, gamma = gamma, scale = scale) at testthat/test-rankFeatures.r:22

9. Error: scoreData (data.frame) (@test-scoreData.r#7) -------------------------
attempt to apply non-function
1: scoreData(data = feature.matrix, model = svm.model) at testthat/test-scoreData.r:7

10. Error: scoreData (genomic.ranges) (@test-scoreData.r#17) -------------------
unused argument (data.granges = crm.features)
1: scoreData(data.granges = crm.features, model = svm.model) at testthat/test-scoreData.r:17

[1] "Takes around 39 seconds in a 4 cored machine with 'Intel(R) Core(TM) i7-3520M CPU @ 2.90GHz'"
11. Error: Tune feature nb (df) (@test-tuneFeatureNb.r#15) ---------------------
unused argument (scale = scale)
1: tuneFeatureNb(data = feature.matrix, cl = 1, feature.rank = feature.ranking, kernel = kernel, 
       valid.times = valid.times, cost = cost, gamma = gamma, scale = scale, step.nb = step.nb) at testthat/test-tuneFeatureNb.r:15

[1] "Takes around 39 seconds in a 4 cored machine with 'Intel(R) Core(TM) i7-3520M CPU @ 2.90GHz'"
12. Error: Tune feature nb (granges) (@test-tuneFeatureNb.r#26) ----------------
unused arguments (data.granges = crm.features, scale = scale)
1: tuneFeatureNb(data.granges = crm.features, cl = 1, feature.rank = feature.ranking, 
       kernel = kernel, valid.times = valid.times, cost = cost, gamma = gamma, scale = scale, 
       step.nb = step.nb) at testthat/test-tuneFeatureNb.r:26

testthat results ================================================================
OK: 45 SKIPPED: 0 FAILED: 12
1. Error: create_model (data.frame) (@test-createModel.r#14) 
2. Error: create_model (genomic.ranges) (@test-createModel.r#24) 
3. Error: evaluate_model_performance (data.frame) (@test-evaluateModelPerformance.r#15) 
4. Error: evaluate_model_performance (data.frame) (@test-evaluateModelPerformance.r#24) 
5. Error: Tune cost gamma (crm.features.tab) (@test-mcTune.r#15) 
6. Error: Tune cost gamma (crm.features.granges) (@test-mcTune.r#26) 
7. Error: Rank features (df) (@test-rankFeatures.r#12) 
8. Error: Rank features (seq.ranges) (@test-rankFeatures.r#22) 
9. Error: scoreData (data.frame) (@test-scoreData.r#7) 
1. ...

Error: testthat unit tests failed
Execution halted

LedPred.Rcheck/00install.out:

* installing *source* package ‘LedPred’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (LedPred)

LedPred.Rcheck/LedPred-Ex.timings:

nameusersystemelapsed
LedPred0.0260.0030.029
createModel0.0030.0010.004
evaluateModelPerformance0.0030.0010.003
mapFeaturesToCRMs0.0010.0010.001
mcTune0.0020.0000.003
rankFeatures0.0020.0010.002
scoreData0.0030.0010.004
tuneFeatureNb0.0030.0010.004