- 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