Check results for 'VGAM'

using R version 2.10.0 Patched (2009-11-03 r50304)
using session charset: UTF-8
checking for file 'VGAM/DESCRIPTION' ... OK
this is package 'VGAM' version '0.7-9'
checking package name space information ... OK
checking package dependencies ... OK
checking if this is a source package ... OK
checking whether package 'VGAM' can be installed ... OK
checking package directory ... OK
checking for portable file names ... OK
checking for sufficient/correct file permissions ... OK
checking DESCRIPTION meta-information ... OK
checking top-level 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 name space can be loaded with stated dependencies ... OK
checking for unstated dependencies in R code ... OK
checking S3 generic/method consistency ... OK
checking replacement functions ... OK
checking foreign function calls ... OK
checking R code for possible problems ... NOTE
Coef.qrrvglm: no visible binding for global variable ‘optimum’
Coef.qrrvglm: no visible binding for global variable ‘Darray’
Coef.qrrvglm: no visible binding for global variable ‘Tolerance’
callcqof: no visible binding for '<<-' assignment to
‘.VGAM.CQO.cmatrix’
callcqof: no visible binding for '<<-' assignment to
‘.VGAM.CQO.ocmatrix’
calldcaof: no visible binding for global variable ‘p1’
calldcaof: no visible binding for global variable ‘U’
calldcaof: no visible binding for global variable ‘queue’
calldcaof: no visible binding for global variable ‘qbig’
calldcaof: no visible binding for global variable ‘spar2’
calldcaof: no visible binding for global variable ‘df2.nl’
cao.fit: no visible binding for global variable ‘maxitl’
cao.fit: no visible binding for global variable ‘fv’
cqo.fit: no visible binding for global variable ‘modelno’
cqo.fit: no visible binding for global variable ‘quasi.newton’
cqo.fit: no visible binding for global variable ‘NOS’
cqo.fit: no visible binding for global variable ‘z’
cqo.fit: no visible binding for global variable ‘fv’
loglinb3 : <anonymous>: no visible binding for global variable ‘u3’
loglinb3 : <anonymous>: no visible binding for global variable ‘u2’
loglinb3 : <anonymous>: no visible binding for global variable ‘u23’
loglinb3 : <anonymous>: no visible binding for global variable ‘u1’
loglinb3 : <anonymous>: no visible binding for global variable ‘u13’
loglinb3 : <anonymous>: no visible binding for global variable ‘u12’
loglinb3 : <anonymous>: no visible binding for global variable ‘denom’
rrvglm.fit: no visible binding for global variable ‘modelno’
rrvglm.fit: no visible binding for global variable ‘fv’
rrvglm.fit: no visible binding for global variable ‘one.more’
rrvglm.fit: no visible binding for global variable ‘rrr.expression’
uqo.fit: no visible binding for global variable ‘CQO.FastAlgorithm’
vgam.fit: no visible binding for global variable ‘fv’
vglm.fit: no visible binding for global variable ‘fv’
checking Rd files ... OK
checking Rd metadata ... OK
checking Rd cross-references ... WARNING
Missing link(s) in documentation object './man/multinomial.Rd':
‘[base]{iris}’

Missing link(s) in documentation object './man/smartpred.Rd':
‘[base]{poly}’

Missing link(s) in documentation object './man/zinegbinomial.Rd':
‘[stats:negative binomial]{rpois}’

See the information in section 'Cross-references' of the 'Writing R
Extensions' manual.
checking for missing documentation entries ... OK
checking for code/documentation mismatches ... OK
checking Rd \usage sections ... OK
checking data for non-ASCII characters ... OK
checking line endings in C/C++/Fortran sources/headers ... OK
checking line endings in Makefiles ... OK
checking for portable use of $BLAS_LIBS ... OK
checking examples ... ERROR
Running examples in 'VGAM-Ex.R' failed.
The error most likely occurred in:

> ### * fff
>
> flush(stderr()); flush(stdout())
>
> ### Name: fff
> ### Title: F Distribution Family Function
> ### Aliases: fff
> ### Keywords: models regression
>
> ### ** Examples
>
> x = runif(n <- 4000)
> df1 = exp(2+0.5*x)
> df2 = exp(2-0.5*x)
> y = rf(n, df1, df2)
> fit = vglm(y ~ x, fff, trace=TRUE)
VGLM linear loop 1 : loglikelihood = -6356.032
VGLM linear loop 2 : loglikelihood = -5099.873
VGLM linear loop 3 : loglikelihood = -5077.138
VGLM linear loop 4 : loglikelihood = -5067.996
755 weight matrices not updated out of 4000
VGLM linear loop 5 : loglikelihood = -5050.141
728 weight matrices not updated out of 4000
VGLM linear loop 6 : loglikelihood = -5041.944
745 weight matrices not updated out of 4000
VGLM linear loop 7 : loglikelihood = -5037.833
865 weight matrices not updated out of 4000
VGLM linear loop 8 : loglikelihood = -5035.856
887 weight matrices not updated out of 4000
VGLM linear loop 9 : loglikelihood = -5034.868
909 weight matrices not updated out of 4000
VGLM linear loop 10 : loglikelihood = -5034.359
914 weight matrices not updated out of 4000
VGLM linear loop 11 : loglikelihood = -5034.09
902 weight matrices not updated out of 4000
VGLM linear loop 12 : loglikelihood = -5033.938
810 weight matrices not updated out of 4000
Warning in vchol(wz, M = M, n = n, silent = !trace) :
weight matrices 352, 1231 not positive-definite
Applying Greenstadt modification to 2 matrices
VGLM linear loop 13 : loglikelihood = -5033.88
454 weight matrices not updated out of 4000
Warning in vchol(wz, M = M, n = n, silent = !trace) :
weight matrix 352 not positive-definite
Applying Greenstadt modification to 1 matrices
Error in lm.fit(X_vlm, z_vlm, ...) :
NA/NaN/Inf in foreign function call (arg 4)
Calls: vglm ... vglm.fitter -> eval -> eval -> vlm.wfit -> lm.fit -> .Fortran
Execution halted