- using R version 3.5.0 (2018-04-23)
- using platform: x86_64-pc-linux-gnu (64-bit)
- using session charset: UTF-8
- checking for file ‘IBHM/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘IBHM’ version ‘1.1-11’
- 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 executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking serialization versions ... OK
- checking whether package ‘IBHM’ can be installed ... OK
- checking package 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 use of S3 registration ... OK
- checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘compiler’
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 ... NOTE
Found the following apparent S3 methods exported but not registered:
length.IBHM predict.IBHM print.summary.IBHM summary.IBHM
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [6s/8s] NOTE
ConfigureIBHM : <anonymous>: no visible global function definition for
‘dnorm’
FindActiv: no visible global function definition for ‘sd’
OptimizeActivCMAES: no visible global function definition for ‘runif’
OptimizeActivNM: no visible global function definition for ‘optim’
OptimizeActivNM: no visible global function definition for ‘runif’
OptimizeAllParams : goal: no visible global function definition for
‘relist’
OptimizeAllParams: no visible global function definition for ‘optim’
OptimizeAllParams: no visible global function definition for ‘relist’
OptimizeAllWeights: no visible global function definition for ‘optim’
OptimizeScalCMAES: no visible global function definition for ‘runif’
OptimizeScalNM: no visible global function definition for ‘optim’
OptimizeScalNM: no visible global function definition for ‘runif’
OptimizeWeights: no visible global function definition for ‘optim’
TrainIBHM: no visible global function definition for ‘enableJIT’
ValidationSC : <anonymous>: no visible global function definition for
‘predict’
group.by.samplesPerDim: no visible global function definition for ‘sd’
summary.IBHM: no visible global function definition for ‘predict’
summary.IBHM: no visible global function definition for ‘sd’
summary.IBHM: no visible global function definition for ‘cor’
Undefined global functions or variables:
cor dnorm enableJIT optim predict relist runif sd
Consider adding
importFrom("stats", "cor", "dnorm", "optim", "predict", "runif", "sd")
importFrom("utils", "relist")
to your NAMESPACE file.
- checking Rd files ... OK
- checking Rd metadata ... OK
- checking Rd line widths ... 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 line endings in C/C++/Fortran sources/headers ... OK
- checking line endings in Makefiles ... OK
- checking compilation flags in Makevars ... OK
- checking for GNU extensions in Makefiles ... OK
- checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
- checking pragmas in C/C++ headers and code ... OK
- checking compilation flags used ... OK
- checking compiled code ... NOTE
File ‘IBHM/libs/IBHM.so’:
Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
It is good practice to register native routines and to disable symbol
search.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
- checking examples ... ERROR
Running examples in ‘IBHM-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ConfigureIBHM
> ### Title: ConfigureIBHM
> ### Aliases: ConfigureIBHM
> ### Keywords: ~models ~regression ~nonlinear
>
> ### ** Examples
>
> x <- seq(-3,3,length.out=400)
> y <- tanh(x)
>
> x.val <- runif(50,min=-6,max=6)
> y.val <- tanh(x.val)
>
> m <- TrainIBHM(x,y, ConfigureIBHM( scal.candidates = 'dot.pr',
+ activ.candidates = 'tanh',
+ stop.criterion = ValidationSC(x.val, y.val)))
>
> summary(m)
Length Class Mode
params 5 -none- list
scals 2 -none- list
activs 2 -none- list
train 2 -none- list
par 5 -none- list
> plot(y.val,predict(m,x.val),asp=1)
Error in UseMethod("predict") :
no applicable method for 'predict' applied to an object of class "IBHM"
Calls: plot -> plot.default -> xy.coords -> predict
Execution halted
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [4s/5s] ERROR
Running ‘ibhm.tests.R’ [3s/5s]
Running the tests in ‘tests/ibhm.tests.R’ failed.
Complete output:
> library(IBHM)
Loading required package: compiler
Loading required package: DEoptim
Loading required package: parallel
DEoptim package
Differential Evolution algorithm in R
Authors: D. Ardia, K. Mullen, B. Peterson and J. Ulrich
Loading required package: cmaes
Loading required package: Rcpp
> source('utils.R')
>
>
> (test.Tanh <- function(){
+ x <- seq(-6,6,length.out=400)
+ y <- tanh(x)
+
+ set.seed(123)
+ m <- TrainIBHM(x,y, ConfigureIBHM(scal.candidates='dot.pr', activ.candidates='tanh'))
+ stopifnot(summary(m)$rmse<0.1)
+ cat('tanh - ok\n')
+ })()
Error in summary(m)$rmse < 0.1 : $ operator is invalid for atomic vectors
Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
- checking PDF version of manual ... OK
- DONE
Status: 2 ERRORs, 4 NOTEs