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SpatialEpiR log file (check_x86_64_linux)

Fri Feb 15 11:39:05 2013: Checking package SpatialEpiR (SVN revision 1026) ...
* using log directory ‘/mnt/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/SpatialEpiR.Rcheck’
* using R version 2.15.2 Patched (2013-02-13 r61942)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘SpatialEpiR/DESCRIPTION’ ... OK
* this is package ‘SpatialEpiR’ version ‘0.0.1’
* package encoding: latin1
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Virgilio Gómez-Rubio ’
New submission
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... WARNING
Subdirectory ‘src’ contains:
  bounds.cmn
These are unlikely file names for src files.
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking whether package ‘SpatialEpiR’ can be installed ... [8s/18s] WARNING
Found the following significant warnings:
  Warning: Deleted feature: Loop variable at (1) must be integer
  Warning: /mnt/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/SpatialEpiR.Rcheck/00_pkg_src/SpatialEpiR/man/siggam.Rd:41: unknown macro '\item'
  Warning: /mnt/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/SpatialEpiR.Rcheck/00_pkg_src/SpatialEpiR/man/siggam.Rd:42: unknown macro '\item'
  Warning: /mnt/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/SpatialEpiR.Rcheck/00_pkg_src/SpatialEpiR/man/siggam.Rd:43: unknown macro '\item'
  Warning: /mnt/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/SpatialEpiR.Rcheck/00_pkg_src/SpatialEpiR/man/siggam.Rd:44: unknown macro '\item'
  Warning: /mnt/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/SpatialEpiR.Rcheck/00_pkg_src/SpatialEpiR/man/siggam.Rd:45: unknown macro '\item'
  Warning: /mnt/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/SpatialEpiR.Rcheck/00_pkg_src/SpatialEpiR/man/siggam.Rd:46: unknown macro '\item'
  Warning: /mnt/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/SpatialEpiR.Rcheck/00_pkg_src/SpatialEpiR/man/siggam.Rd:49: unknown macro '\item'
  Warning: /mnt/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/SpatialEpiR.Rcheck/00_pkg_src/SpatialEpiR/man/siggam.Rd:51: unknown macro '\item'
  Warning: /mnt/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/SpatialEpiR.Rcheck/00_pkg_src/SpatialEpiR/man/siggam.Rd:52: unknown macro '\item'
  Warning: /mnt/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/SpatialEpiR.Rcheck/00_pkg_src/SpatialEpiR/man/siggam.Rd:53: unknown macro '\item'
  Warning: /mnt/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/SpatialEpiR.Rcheck/00_pkg_src/SpatialEpiR/man/siggam.Rd:55: unknown macro '\item'
  Warning: /mnt/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/SpatialEpiR.Rcheck/00_pkg_src/SpatialEpiR/man/siggam.Rd:56: unknown macro '\item'
  running .First.lib() for package ‘SpatialEpiR’ as .onLoad/.onAttach were not found
See ‘/mnt/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/SpatialEpiR.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
  GPL Version 2 or later.
Standardizable: TRUE
Standardized license specification:
  GPL (>= 2)
* 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 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
File ‘SpatialEpiR/R/First.lib.R’:
  .First.lib calls:
    cat("\nSPatialEpiR alpha-test version\n")

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in ?.onAttach.

computeint: no visible global function definition for ‘lambdahat’
computeint2: no visible global function definition for ‘adapt’
cvbinreg: no visible global function definition for ‘setkernel’
cvbinreg: no visible global function definition for ‘lambdahat’
fitloggam: no visible binding for global variable ‘fstart’
fitloggam: no visible binding for global variable ‘pstart’
siggam: no visible binding for global variable ‘ngrid’
* checking Rd files ... WARNING
prepare_Rd: calcvarbeta.Rd:62: Dropping empty section \keyword
prepare_Rd: cvkernratio.Rd:45: Dropping empty section \keyword
prepare_Rd: cvkernratio.Rd:42-43: Dropping empty section \references
prepare_Rd: fitloggam.Rd:44: Dropping empty section \keyword
prepare_Rd: fitsmacc.Rd:57: Dropping empty section \keyword
prepare_Rd: fitsmacc.Rd:43-45: Dropping empty section \examples
prepare_Rd: fitwam.Rd:47: Dropping empty section \keyword
prepare_Rd: hch2d.Rd:47: Dropping empty section \keyword
prepare_Rd: kdespat.Rd:75-77: Dropping empty section \keyword
prepare_Rd: kdespat.Rd:70-72: Dropping empty section \references
prepare_Rd: keredgecor.Rd:38: Dropping empty section \keyword
prepare_Rd: kerreg2d.Rd:49: Dropping empty section \keyword
prepare_Rd: kerreg2d.Rd:44-46: Dropping empty section \references
prepare_Rd: matched.Rd:54: Dropping empty section \keyword
prepare_Rd: matched.Rd:44-46: Dropping empty section \examples
prepare_Rd: minh.Rd:55: Dropping empty section \keyword
prepare_Rd: plotrisk.Rd:54: Dropping empty section \keyword
prepare_Rd: plotrisk.Rd:48-51: Dropping empty section \references
prepare_Rd: relrisk.Rd:60: Dropping empty section \keyword
prepare_Rd: siggam.Rd:41: unknown macro '\item'
prepare_Rd: siggam.Rd:42: unknown macro '\item'
prepare_Rd: siggam.Rd:43: unknown macro '\item'
prepare_Rd: siggam.Rd:44: unknown macro '\item'
prepare_Rd: siggam.Rd:45: unknown macro '\item'
prepare_Rd: siggam.Rd:46: unknown macro '\item'
prepare_Rd: siggam.Rd:49: unknown macro '\item'
prepare_Rd: siggam.Rd:51: unknown macro '\item'
prepare_Rd: siggam.Rd:52: unknown macro '\item'
prepare_Rd: siggam.Rd:53: unknown macro '\item'
prepare_Rd: siggam.Rd:55: unknown macro '\item'
prepare_Rd: siggam.Rd:56: unknown macro '\item'
prepare_Rd: siggam.Rd:74: Dropping empty section \keyword
prepare_Rd: siggam.Rd:64-66: Dropping empty section \examples
prepare_Rd: tolplot.Rd:34: Dropping empty section \keyword
prepare_Rd: tolplot.Rd:31-32: Dropping empty section \references
prepare_Rd: tolplot.Rd:28-29: Dropping empty section \examples
prepare_Rd: tolsmacc.Rd:54: Dropping empty section \keyword
prepare_Rd: tolsmacc.Rd:50-52: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘computeint’ ‘computeint2’ ‘cvbinreg’ ‘logr’
All user-level objects in a package should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... WARNING
Argument items with no description in Rd object 'calcvarbeta':
  ‘outermax’ ‘innermax’ ‘tolbeta’ ‘tolg’ ‘rings’ ‘denspts’ ‘randomseed’

Argument items with no description in Rd object 'fitsmacc':
  ‘ngrid’ ‘outermax’ ‘innermax’ ‘tolbeta’ ‘tolg’ ‘rings’ ‘denspts’

Argument items with no description in Rd object 'tolsmacc':
  ‘outermax’ ‘innermax’ ‘tolbeta’ ‘tolg’ ‘rings’ ‘denspts’ ‘randomseed’

* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/mnt/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/SpatialEpiR.Rcheck/SpatialEpiR/libs/SpatialEpiR.so’:
  Found ‘printf’, possibly from ‘printf’ (C)
    Object: ‘smaccalc.o’
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Objects: ‘allofree.o’, ‘matfunc.o’, ‘newt.o’, ‘smaccalc.o’

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... ERROR
Running examples in ‘SpatialEpiR-Ex.R’ failed
The error most likely occurred in:

> ### Name: cvkernratio
> ### Title: Estimate optimal bandwidth for a case-control point pattern
> ###   using a cross-validation criterion.
> ### Aliases: cvkernratio
> 
> ### ** Examples
> 
> data(southlancs)
> 
> ncases<-sum(southlancs.cc==1)
> ncontrols<-sum(southlancs.cc==0)
> ccpts<-southlancs.pts[nrow(southlancs.pts):1,]
> h<-seq(1600, 1800, by=50)
> 
> cvres<-cvkernratio(ccpts, ncases, ncontrols, southlancs.bdy, 
+    h=h, kernel="normal", edge=FALSE)
Error in computeint2(ccpts[idxcases, ], ccpts[idxcontrols, ], pbdry, hbw,  : 
  could not find function "adapt"
Calls: cvkernratio -> computeint2
Execution halted
Run time: 82.14 seconds.
Additional Logs:   00install.out
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