MLInterfaces 1.49.11
V. Carey
| Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MLInterfaces | | Last Changed Rev: 107688 / Revision: 107696 | | Last Changed Date: 2015-08-22 06:37:06 -0700 (Sat, 22 Aug 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 | [ ERROR ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | ERROR | 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 MLInterfaces_1.49.11.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/MLInterfaces.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MLInterfaces/DESCRIPTION’ ... OK
* this is package ‘MLInterfaces’ version ‘1.49.11’
* 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 ‘MLInterfaces’ can be installed ... [17s/17s] 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘ada:::predict.ada’ ‘e1071:::predict.svm’ ‘MASS:::predict.lda’
‘rpart:::predict.rpart’ ‘stats:::plot.hclust’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
hclustWidget : <anonymous>: no visible global function definition for
‘:=’
hclustWidget : <anonymous>: no visible binding for global variable
‘key’
* checking Rd files ... NOTE
prepare_Rd: plspinHcube.Rd:17-19: Dropping empty section \details
* 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 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 ‘MLInterfaces-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: projectLearnerToGrid
> ### Title: create learned tesselation of feature space after PC
> ### transformation
> ### Aliases: projectLearnerToGrid
> ### Keywords: models
>
> ### ** Examples
>
> library(mlbench)
> # demostrate with 3 dimensional hypercube problem
> kk = mlbench.hypercube()
> colnames(kk$x) = c("f1", "f2", "f3")
> hcu = data.frame(cl=kk$classes, kk$x)
> library(MLInterfaces)
> set.seed(1234)
> sam = sample(1:nrow(kk$x), size=nrow(kk$x)/2)
> ldap = projectLearnerToGrid(cl˜., data=hcu, ldaI,
+ sam, predWrapper=function(x)x$class)
> plot(ldap)
> confuMat(ldap@fittedLearner)
predicted
given 1 2 3 4 5 6 7 8
1 52 0 0 0 0 0 0 0
2 0 46 0 0 0 0 0 0
3 0 0 48 0 0 0 0 0
4 0 0 0 49 0 0 0 0
5 0 0 0 0 48 0 0 0
6 0 0 0 0 0 60 0 0
7 0 0 0 0 0 0 49 0
8 0 0 0 0 0 0 0 48
> nnetp = projectLearnerToGrid(cl˜., data=hcu, nnetI, sam, size=2,
+ decay=.01, predExtras=list(type="class"))
# weights: 32
initial value 870.074507
iter 10 value 424.595414
iter 20 value 247.935684
iter 30 value 181.687349
iter 40 value 127.244873
iter 50 value 119.190019
iter 60 value 90.073203
iter 70 value 83.210358
iter 80 value 82.748647
iter 90 value 81.799785
iter 100 value 81.670631
final value 81.670631
stopped after 100 iterations
> plot(nnetp)
> confuMat(nnetp@fittedLearner)
predicted
given 1 2 3 4 5 6 7 8
1 51 0 1 0 0 0 0 0
2 0 43 2 0 0 0 1 0
3 0 0 48 0 0 0 0 0
4 0 0 0 49 0 0 0 0
5 0 0 0 0 48 0 0 0
6 0 0 0 0 0 60 0 0
7 0 0 0 0 4 2 43 0
8 0 0 0 0 0 0 0 48
> if (require(rgl)) {
+ learnerIn3D(nnetp)
+ ## customising the rgl plot
+ learnerIn3D(nnetp, size = 10, alpha = 0.1)
+ }
Loading required package: rgl
Error in rgl.open(useNULL) : rgl.open failed
Calls: learnerIn3D ... plot3d.default -> next3d -> .check3d -> open3d -> rgl.open
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [8s/8s]
[9s/9s] OK
* 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
‘/Users/biocbuild/bbs-3.2-bioc/meat/MLInterfaces.Rcheck/00check.log’
for details.
* installing *source* package ‘MLInterfaces’ ...
** 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
** installing vignettes
** 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 (MLInterfaces)