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BioC 3.2: CHECK report for stepwiseCM on perceval

This page was generated on 2015-10-27 17:34:48 -0400 (Tue, 27 Oct 2015).

Package 1026/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
stepwiseCM 1.16.0
Askar Obulkasim
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/stepwiseCM
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: stepwiseCM
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings stepwiseCM_1.16.0.tar.gz
StartedAt: 2015-10-27 12:41:25 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 12:44:28 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 182.1 seconds
RetCode: 0
Status:  OK 
CheckDir: stepwiseCM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings stepwiseCM_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/stepwiseCM.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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’ ‘e1071’ ‘glmpath’ ‘MAclinical’ ‘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 ... [121s/121s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
Step.pred          27.260  0.502  27.764
stepwiseCM-package 27.018  0.306  27.326
Curve.generator    26.584  0.465  27.069
RS.generator       24.171  0.288  24.460
Classifier         10.241  0.271  10.513
* 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: 3 NOTEs
See
  ‘/Users/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
CNS0.2070.0150.222
Classifier10.241 0.27110.513
Classifier.par0.1820.0160.199
Curve.generator26.584 0.46527.069
Proximity0.2490.0100.259
RS.generator24.171 0.28824.460
Step.pred27.260 0.50227.764
stepwiseCM-package27.018 0.30627.326