ConsPlan - Conservation planning optimization - check results
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ConsPlan

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Version: 0.1
Result: ERROR
Check time: 2014-03-29 14:09
* using log directory ''
* using R Under development (unstable) (2014-03-29 r65336)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* checking for file 'ConsPlan/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ConsPlan' version '0.1'
* 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 whether package 'ConsPlan' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
GPL version 2 or newer
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 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'sann'
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 ... WARNING
Objects in \usage without \alias in documentation object 'sann':
'sann'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking examples ... ERROR
Running examples in 'ConsPlan-Ex.R' failed
The error most likely occurred in:

> ### Name: sann
> ### Title: Simulated Anneal Optimization
> ### Aliases: lcmw
>
> ### ** Examples
>
>
> ## Traveling salesman problem (modified from \code{optim})
> library(stats) # normally loaded
>
> eurodistmat <- as.matrix(eurodist)
>
> distance <- function(sq) { # Target function
+ sq2 <- embed(sq, 2)
+ return(as.numeric(sum(eurodistmat[cbind(sq2[,2],sq2[,1])])))
+ }
>
> genseq <- function(sq) { # Generate new candidate sequence
+ idx <- seq(2, NROW(eurodistmat)-1, by=1)
+ changepoints <- sample(idx, size=2, replace=FALSE)
+ tmp <- sq[changepoints[1]]
+ sq[changepoints[1]] <- sq[changepoints[2]]
+ sq[changepoints[2]] <- tmp
+ return(as.numeric(sq))
+ }
>
> sq <- c(1,2:NROW(eurodistmat),1) # Initial sequence
> distance(sq)
[1] 29625
>
> set.seed(123) # chosen to get a good soln relatively quickly
> res <- sann(sq, distance, genseq, maxit=30000, REPORT=500, temp=2000)
initial value 29625.000000
iter 5000 value 13585.000000
iter 10000 value 13092.000000
Error in sann(sq, distance, genseq, maxit = 30000, REPORT = 500, temp = 2000) :
REAL() can only be applied to a 'numeric', not a 'builtin'
Calls: sann -> .Call
Execution halted

Installation log: 00install.out

Distribution log

SVN checkout/GIT clone log


Build log for Mac OS X 10.5 (R 2.16.x)

* installing *source* package 'ConsPlan' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c sann.c -o sann.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o ConsPlan.so sann.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Volumes/Tiger/Builds/rforge/Rlib/osx9-2.16/ConsPlan/libs/i386
*** arch - ppc
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c sann.c -o sann.o
gcc -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o ConsPlan.so sann.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Volumes/Tiger/Builds/rforge/Rlib/osx9-2.16/ConsPlan/libs/ppc
*** arch - x86_64
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c sann.c -o sann.o
gcc -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o ConsPlan.so sann.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Volumes/Tiger/Builds/rforge/Rlib/osx9-2.16/ConsPlan/libs/x86_64
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
*** arch - ppc
*** arch - x86_64
packaged installation of 'ConsPlan' as 'ConsPlan_0.1.tgz'

* DONE (ConsPlan)

Build log for Windows 7 (R 3.0.x)

(ConsPlan 0.1)
* installing to library 'z:/rforge/Rlib/win7-3.0'
* installing *source* package 'ConsPlan' ...
** libs

*** arch - i386
gcc -m32 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c sann.c -o sann.o
gcc -m32 -shared -s -static-libgcc -o ConsPlan.dll tmp.def sann.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/PROGRA~1/r/r-3.0/bin/i386 -lR
installing to z:/rforge/Rlib/win7-3.0/ConsPlan/libs/i386

*** arch - x64
gcc -m64 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c sann.c -o sann.o
gcc -m64 -shared -s -static-libgcc -o ConsPlan.dll tmp.def sann.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/PROGRA~1/r/r-3.0/bin/x64 -lR
installing to z:/rforge/Rlib/win7-3.0/ConsPlan/libs/x64
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* MD5 sums
packaged installation of 'ConsPlan' as ConsPlan_0.1.zip
* DONE (ConsPlan)