a4Classif 1.18.0
Tobias Verbeke , Willem Ligtenberg
| Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/a4Classif | | Last Changed Rev: 109589 / Revision: 110496 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings a4Classif_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/a4Classif.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 ‘a4Classif/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘a4Classif’ version ‘1.18.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘a4Core’ ‘a4Preproc’ ‘MLInterfaces’ ‘ROCR’ ‘pamr’ ‘glmnet’ ‘varSelRF’
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 ‘a4Classif’ can be installed ... [0m/11m] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘a4Core’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
‘a4Preproc’ ‘glmnet’ ‘methods’ ‘MLInterfaces’ ‘pamr’ ‘ROCR’
‘varSelRF’
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
confusionMatrix.pamClass: no visible global function definition for
‘pamr.confusion’
lassoClass: no visible global function definition for ‘pData’
lassoClass: no visible global function definition for ‘glmnet’
lassoClass: no visible global function definition for ‘exprs’
lassoClass: no visible global function definition for ‘featureData’
pamClass: no visible global function definition for ‘pData’
pamClass: no visible global function definition for ‘featureNames’
pamClass: no visible global function definition for ‘exprs’
pamClass: no visible global function definition for ‘pamr.train’
pamClass: no visible global function definition for ‘pamr.cv’
pamClass: no visible global function definition for ‘featureData’
rfClass: no visible global function definition for ‘pData’
rfClass: no visible global function definition for ‘varSelRF’
rfClass: no visible global function definition for ‘exprs’
rfClass: no visible global function definition for ‘featureData’
rfClass: no visible global function definition for ‘featureNames’
ROCcurve: no visible global function definition for ‘exprs’
ROCcurve: no visible global function definition for ‘featureData’
ROCcurve: no visible global function definition for ‘featureNames’
ROCcurve: no visible global function definition for ‘pData’
ROCcurve: no visible global function definition for ‘prediction’
ROCcurve: no visible global function definition for ‘performance’
topTable,pamClass : .local: no visible global function definition for
‘pamr.listgenes’
* 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 examples ... [18s/23s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
ROCcurve 4.087 0.109 8.023
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.2-bioc/meat/a4Classif.Rcheck/00check.log’
for details.
* installing *source* package ‘a4Classif’ ...
** R
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : Error in 'rgl_init'
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : Error in 'rgl_init'
* DONE (a4Classif)