stepwiseCM 1.23.1
Askar Obulkasim
| Snapshot Date: 2017-10-29 17:00:18 -0400 (Sun, 29 Oct 2017) | | URL: https://git.bioconductor.org/packages/stepwiseCM | | Branch: master | | Last Commit: 5a7933b | | Last Changed Date: 2017-04-24 19:27:36 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ ERROR ] | | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | ERROR | OK | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | ERROR | skipped | skipped | |
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --no-vignettes --timings stepwiseCM_1.23.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/stepwiseCM.Rcheck’
* using R Under development (unstable) (2017-10-20 r73567)
* 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 ‘1.23.1’
* 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 ... WARNING
Found the following significant warnings:
Warning: Package 'stepwiseCM' is deprecated and will be removed from
See ‘/home/biocbuild/bbs-3.7-bioc/meat/stepwiseCM.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 ... 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
‘predict’
.Wrapper.Classifier: no visible global function definition for
‘cv.glmpath’
.Wrapper.Classifier: no visible binding for global variable ‘binomial’
.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 ‘predict’
Classifier: no visible global function definition for ‘cv.glmpath’
Classifier: no visible binding for global variable ‘binomial’
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’
Curve.generator: no visible global function definition for ‘plot’
Curve.generator: no visible global function definition for ‘points’
Curve.generator: no visible global function definition for ‘legend’
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’
Undefined global functions or variables:
binomial cv.glmpath exprs glmpath legend optL1 optL2 pamr.cv
pamr.listgenes pamr.predict pamr.train penalized plot plsrf_x
plsrf_x_pv points predict predict.glmpath randomForest sfExportAll
sfInit sfLapply sfLibrary sfStop stepwiseCM svm tspcalc tune.control
tune.svm
Consider adding
importFrom("graphics", "legend", "plot", "points")
importFrom("stats", "binomial", "predict")
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 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: element-wise multiplication: incompatible matrix dimensions: 20x1 and 1x20
Error in .steplasso(beta = beta, lambda = lambda1, positive = positive, :
element-wise multiplication: incompatible matrix dimensions: 20x1 and 1x20
Calls: Classifier ... ifelse -> f -> .cvl -> cvfit -> .steplasso -> .Call
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, 3 NOTEs
See
‘/home/biocbuild/bbs-3.7-bioc/meat/stepwiseCM.Rcheck/00check.log’
for details.
* 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
Warning: Package 'stepwiseCM' is deprecated and will be removed from
Bioconductor version 3.7
* DONE (stepwiseCM)