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BioC 3.2: CHECK report for stepwiseCM on zin1

This page was generated on 2016-04-23 10:12:13 -0700 (Sat, 23 Apr 2016).

Package 1026/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
stepwiseCM 1.16.0
Askar Obulkasim
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/stepwiseCM
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ ERROR ]
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  ERROR  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  ERROR  OK 

Summary

Package: stepwiseCM
Version: 1.16.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings stepwiseCM_1.16.0.tar.gz
StartedAt: 2016-04-23 05:50:47 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 05:51:54 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 66.6 seconds
RetCode: 1
Status:  ERROR 
CheckDir: stepwiseCM.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings stepwiseCM_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/stepwiseCM.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘stepwiseCM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘stepwiseCM’ version ‘1.16.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘randomForest’ ‘MAclinical’ ‘tspair’ ‘pamr’ ‘snowfall’ ‘glmpath’
  ‘penalized’ ‘e1071’ ‘Biobase’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘stepwiseCM’ can be installed ... [6s/6s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘MAclinical’ ‘e1071’ ‘glmpath’ ‘pamr’ ‘penalized’
  ‘randomForest’ ‘snowfall’ ‘tspair’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.Wrapper.Classifier: no visible global function definition for
  ‘tspcalc’
.Wrapper.Classifier: no visible global function definition for
  ‘cv.glmpath’
.Wrapper.Classifier: no visible global function definition for
  ‘glmpath’
.Wrapper.Classifier: no visible global function definition for
  ‘predict.glmpath’
.Wrapper.Classifier: no visible global function definition for ‘optL1’
.Wrapper.Classifier: no visible global function definition for
  ‘penalized’
.Wrapper.Classifier: no visible global function definition for ‘optL2’
.Wrapper.Classifier: no visible global function definition for
  ‘pamr.train’
.Wrapper.Classifier: no visible global function definition for
  ‘pamr.cv’
.Wrapper.Classifier: no visible global function definition for
  ‘pamr.predict’
.Wrapper.Classifier: no visible global function definition for
  ‘tune.svm’
.Wrapper.Classifier: no visible global function definition for
  ‘tune.control’
.Wrapper.Classifier: no visible global function definition for ‘svm’
.Wrapper.Classifier: no visible global function definition for
  ‘plsrf_x’
.Wrapper.Classifier: no visible global function definition for
  ‘plsrf_x_pv’
.Wrapper.Classifier: no visible global function definition for
  ‘randomForest’
.Wrapper.Proximity: no visible global function definition for
  ‘randomForest’
Classifier: no visible global function definition for ‘exprs’
Classifier: no visible global function definition for ‘tspcalc’
Classifier: no visible global function definition for ‘cv.glmpath’
Classifier: no visible global function definition for ‘glmpath’
Classifier: no visible global function definition for ‘predict.glmpath’
Classifier: no visible global function definition for ‘optL1’
Classifier: no visible global function definition for ‘penalized’
Classifier: no visible global function definition for ‘optL2’
Classifier: no visible global function definition for ‘pamr.train’
Classifier: no visible global function definition for ‘pamr.cv’
Classifier: no visible global function definition for ‘pamr.predict’
Classifier: no visible global function definition for ‘pamr.listgenes’
Classifier: no visible global function definition for ‘tune.svm’
Classifier: no visible global function definition for ‘tune.control’
Classifier: no visible global function definition for ‘svm’
Classifier: no visible global function definition for ‘plsrf_x’
Classifier: no visible global function definition for ‘plsrf_x_pv’
Classifier: no visible global function definition for ‘randomForest’
Classifier.par: no visible global function definition for ‘exprs’
Classifier.par: no visible global function definition for ‘sfInit’
Classifier.par: no visible global function definition for ‘sfLibrary’
Classifier.par: no visible binding for global variable ‘stepwiseCM’
Classifier.par: no visible global function definition for ‘sfExportAll’
Classifier.par: no visible global function definition for ‘sfLapply’
Classifier.par: no visible global function definition for ‘sfStop’
Proximity: no visible global function definition for ‘exprs’
Proximity: no visible global function definition for ‘randomForest’
Proximity: no visible global function definition for ‘sfInit’
Proximity: no visible global function definition for ‘sfLibrary’
Proximity: no visible binding for global variable ‘randomForest’
Proximity: no visible binding for global variable ‘stepwiseCM’
Proximity: no visible global function definition for ‘sfExportAll’
Proximity: no visible global function definition for ‘sfLapply’
Proximity: no visible global function definition for ‘sfStop’
* 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 ... ERROR
Running examples in ‘stepwiseCM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Classifier
> ### Title: A function to perform classification task.
> ### Aliases: Classifier
> 
> ### ** Examples
> 
> data(CNS)
> train <- CNS$mrna[, 1:40]
> test <- CNS$mrna[, 41:60]
> train.label <- CNS$class[1:40]
> Pred <- Classifier(train = train, test = test, train.label = train.label, 
+         type = "GLM_L1", CVtype = "k-fold", outerkfold = 2, innerkfold = 2)
Error in .local(object, ...) : 
  row counts of "penalized", "unpenalized" and/or "data" do not match
Calls: Classifier -> predict -> predict -> .local
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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/stepwiseCM.Rcheck/00check.log’
for details.

stepwiseCM.Rcheck/00install.out:

* installing *source* package ‘stepwiseCM’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (stepwiseCM)

stepwiseCM.Rcheck/stepwiseCM-Ex.timings:

nameusersystemelapsed
CNS0.1760.0000.177