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glmmGS log file (check_x86_64_linux)

Fri Oct 16 17:25:23 2015: Checking package glmmGS (SVN revision 155) ...
* using log directory ‘/mnt/building/build_2015-10-16-17-24/RF_PKG_CHECK/PKGS/glmmGS.Rcheck’
* using R version 3.2.2 Patched (2015-10-15 r69519)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘glmmGS/DESCRIPTION’ ... OK
* this is package ‘glmmGS’ version ‘0.6-118’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Michele Morara’

CRAN repository db overrides:
  SystemRequirements: GNU make
Found the following (possibly) invalid URLs:
  URL: http://www.cise.ufl.edu/research/sparse/amd/
    From: man/glmmGS.SparseMatrix.Rd
    Status: 404
    Message: Not Found
  URL: http://www.cise.ufl.edu/research/sparse/ldl/
    From: man/glmmGS.SparseMatrix.Rd
    Status: 404
    Message: Not Found

The Title field should be in title case, current version then in title case:
‘Gauss-Seidel Generalized Linear Mixed Model solver’
‘Gauss-Seidel Generalized Linear Mixed Model Solver’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
  No repository set, so cyclic dependency check skipped
* 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 whether package ‘glmmGS’ can be installed ... [17s/19s] 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.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Calls with DUP:
   .C("GlmmGSRAPI_AddCountsInt", values, size, DUP = FALSE, NAOK = FALSE, 
       PACKAGE = "glmmGS")
   .C("GlmmGSRAPI_AddCovariateInt", values, size, duplicate, DUP = FALSE, 
       NAOK = FALSE, PACKAGE = "glmmGS")
   .C("GlmmGSRAPI_AddCovariateDbl", values, size, duplicate, DUP = FALSE, 
       NAOK = FALSE, PACKAGE = "glmmGS")
   .C("GlmmGSRAPI_AddCovariatesInt", values, dim, duplicate, DUP = FALSE, 
       NAOK = FALSE, PACKAGE = "glmmGS")
   .C("GlmmGSRAPI_AddCovariatesDbl", values, dim, duplicate, DUP = FALSE, 
       NAOK = FALSE, PACKAGE = "glmmGS")
   .C("GlmmGSRAPI_AddIdentityModel", theta, len.theta, DUP = FALSE, 
       NAOK = FALSE, PACKAGE = "glmmGS")
   .C("GlmmGSRAPI_AddMultivariateIdentityModel", theta, len.theta, 
       DUP = FALSE, NAOK = FALSE, PACKAGE = "glmmGS")
   .C("GlmmGSRAPI_AddOffsetInt", values, size, DUP = FALSE, NAOK = FALSE, 
       PACKAGE = "glmmGS")
   .C("GlmmGSRAPI_AddOffsetDbl", values, size, DUP = FALSE, NAOK = FALSE, 
       PACKAGE = "glmmGS")
   .C("GlmmGSRAPI_AddPrecisionModel", R, dim.R, theta, len.theta, 
       DUP = FALSE, NAOK = FALSE, PACKAGE = "glmmGS")
   .C("GlmmGSRAPI_AddResponseInt", values, size, DUP = FALSE, NAOK = FALSE, 
       PACKAGE = "glmmGS")
   .C("GlmmGSRAPI_AddResponseDbl", values, size, DUP = FALSE, NAOK = FALSE, 
       PACKAGE = "glmmGS")
   .C("GlmmGSRAPI_AddSparsePrecisionModel", sparse.R$values, sparse.R$indices, 
       sparse.R$counts, ncols, theta, len.theta, DUP = FALSE, NAOK = FALSE, 
       PACKAGE = "glmmGS")
   .C("GlmmGSRAPI_BeginStratifiedBlock", levels, size, DUP = FALSE, 
       NAOK = FALSE, PACKAGE = "glmmGS")
   .C("GlmmGSRAPI_GetFixefDenseBlock", index, estm, vcov, nvars, 
       DUP = FALSE, NAOK = FALSE, PACKAGE = "glmmGS")
   .C("GlmmGSRAPI_GetFixefStratifiedBlock", index, estm, vcov, nvars, 
       nlevels, DUP = FALSE, NAOK = FALSE, PACKAGE = "glmmGS")
   .C("GlmmGSRAPI_GetIterations", iterations, size, DUP = FALSE, 
       NAOK = FALSE, PACKAGE = "glmmGS")
   .C("GlmmGSRAPI_GetRanefDenseBlock", index, estm, nvars, DUP = FALSE, 
       NAOK = FALSE, PACKAGE = "glmmGS")
   .C("GlmmGSRAPI_GetVCompDenseBlock", index, estm, vcov, size, 
       DUP = FALSE, NAOK = FALSE, PACKAGE = "glmmGS")
   .C("GlmmGSRAPI_GetRanefStratifiedBlock", index, estm, nvars, 
       nlevels, DUP = FALSE, NAOK = FALSE, PACKAGE = "glmmGS")
   .C("GlmmGSRAPI_GetVCompStratifiedBlock", index, estm, vcov, size, 
       DUP = FALSE, NAOK = FALSE, PACKAGE = "glmmGS")
DUP is no longer supported and will be ignored.
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
prepare_Rd: fixef.Rd:23-25: Dropping empty section \details
prepare_Rd: fixef.Rd:45-47: Dropping empty section \note
prepare_Rd: fixef.Rd:38-40: Dropping empty section \references
prepare_Rd: fixef.Rd:51-53: Dropping empty section \seealso
prepare_Rd: glmmGS.Control.Rd:83-85: Dropping empty section \note
prepare_Rd: glmmGS.Control.Rd:76-78: Dropping empty section \references
prepare_Rd: glmmGS.CovarianceModel.Rd:42-44: Dropping empty section \details
prepare_Rd: glmmGS.CovarianceModel.Rd:60-62: Dropping empty section \note
prepare_Rd: glmmGS.CovarianceModel.Rd:53-55: Dropping empty section \references
prepare_Rd: glmmGS.Rd:63-65: Dropping empty section \details
prepare_Rd: glmmGS.SparseMatrix.Rd:57-59: Dropping empty section \note
prepare_Rd: ranef.Rd:23-25: Dropping empty section \details
prepare_Rd: ranef.Rd:45-47: Dropping empty section \note
prepare_Rd: ranef.Rd:38-40: Dropping empty section \references
prepare_Rd: ranef.Rd:51-53: Dropping empty section \seealso
prepare_Rd: vcomp.Rd:23-25: Dropping empty section \details
prepare_Rd: vcomp.Rd:43-45: Dropping empty section \note
prepare_Rd: vcomp.Rd:36-38: Dropping empty section \references
prepare_Rd: vcomp.Rd:49-51: Dropping empty section \seealso
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'glmmGS.CovarianceModel.Rd':
  \examples lines wider than 100 characters:
             # Set a vector of precision parameters to be used with two correlated random effect variables
             I.mv.fixed <- glmmGS.CovarianceModel("identity", within = "multivariate", fix.components = true.theta)

Rd file 'glmmGS.Rd':
  \examples lines wider than 100 characters:
             levels(dayOfWeek) <- c("Monday", "Tuesday", "Wednesday", "Thursday", "Friday", "Saturday", "Sunday")
             I.mv.fixed <- glmmGS.CovarianceModel("identity", within = "multivariate", fix.components = true.theta)

These lines will be truncated in the PDF manual.
* 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 ... WARNING
Found the following file(s) containing GNU extensions:
  src/Makevars
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking examples ... ERROR
Running examples in ‘glmmGS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fixef
> ### Title: Extract fixed effect estimates
> ### Aliases: fixef
> ### Keywords: ~kwd1 ~kwd2
> 
> ### ** Examples
> 
> 	# Run glmmGS example producing the variable 'result1' and 'result2'
> 	example(glmmGS)

glmmGS> 	# Set data dimension: 
glmmGS> 	# - 1 million observations, 
glmmGS> 	# - 7 day-of-the-week specific fixed effects
glmmGS> 	# - 2000 post-code specific random effects
glmmGS> 	nobs <- 1000000L

glmmGS> 	nDaysOfWeek <- 7L

glmmGS> 	nPostCodes <- 2000L

glmmGS> 	# Generate data
glmmGS> 	set.seed(23)

glmmGS> 	# Size of binomial observations
glmmGS> 	size <- as.integer(runif(nobs, 1, 10))

glmmGS> 	# Covariate
glmmGS> 	x <- rnorm(nobs)

glmmGS> 	# Fixed effects and random effects grouping factors
glmmGS> 	dayOfWeek <- factor(as.integer(runif(nobs, 1, nDaysOfWeek + 1))) 

glmmGS> 	postCode <- factor(as.integer(runif(nobs, 1, nPostCodes + 1)))

glmmGS> 	# Set level names for dayOfWeek factor
glmmGS> 	levels(dayOfWeek) <- c("Monday", "Tuesday", "Wednesday", "Thursday", "Friday", "Saturday", "Sunday")

glmmGS> 	# Generate fixed effects
glmmGS> 	beta0 <- -0.5

glmmGS> 	beta1 <- 0.7

glmmGS> 	betaDays <- rnorm(nDaysOfWeek, sd = 0.1)

glmmGS> 	betaDays[1] <- 0 # Set first level equal to zero

glmmGS> 	# Generate random effects
glmmGS> 	b0 <- rnorm(nPostCodes, sd = sqrt(0.02))

glmmGS> 	b1 <- rnorm(nPostCodes, sd = sqrt(0.01))

glmmGS> 	# Generate linear predictor
glmmGS> 	eta <- beta0 + x * beta1

glmmGS> 	eta <- eta + betaDays[as.integer(dayOfWeek)]

glmmGS> 	eta <- eta + b0[as.integer(postCode)] + x * b1[as.integer(postCode)]

glmmGS> 	# Generate response
glmmGS> 	y <- as.integer(rbinom(nobs, size, plogis(eta)))

glmmGS> 	# Define identity covariance model
glmmGS> 	I <- glmmGS.CovarianceModel("identity")

glmmGS> 	# Define control list
glmmGS> 	control <- glmmGS.Control(reltol = 1.e-6, abstol = 1.e-6, maxit = 200, verbose = FALSE)

glmmGS> 	# Fit model using Gauss-Seidel algorithm with three blocks: 
glmmGS> 	# - one dense fixed effect block: (1 + x);
glmmGS> 	# - one stratified fixed effect block: (1 | dayOfWeek);
glmmGS> 	# - one stratified random effect block: (1 + x | postCode ~ I)
glmmGS> 	#   with an identity prior covariance matrix
glmmGS> 	result1 <- glmmGS((y / size) ~ (1 + x) + (1 | dayOfWeek) + (1 + x | postCode ~ I), 
glmmGS+ 		family = binomial, control = control)
Error in glmmGSAPI.GetLastError() : 
  Non positive matrix in Cholesky decomposition
Calls: example ... eval -> glmmGS -> glmmGSAPI.Fit -> glmmGSAPI.GetLastError
Execution halted
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 6 NOTEs
See
  ‘/mnt/building/build_2015-10-16-17-24/RF_PKG_CHECK/PKGS/glmmGS.Rcheck/00check.log’
for details.

Run time: 43.85 seconds.