Can't run demo in wiki because of populationdynamics package

cboettig / earlywarning

:notebook: Methods for detecting early warning signals of critical transitions

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> install_github("populationdynamics", "cboettig") Installing populationdynamics from cboettig Installing populationdynamics * checking for file '/private/var/folders/69/7ztsqtsx4js1m7y_mhcrgmdw0000gn/T/RtmpMlTTfy/cboettig-populationdynamics-efc1ef7/DESCRIPTION' ... OK * preparing 'populationdynamics': * checking DESCRIPTION meta-information ... OK * cleaning src * checking for LF line-endings in source and make files * checking for empty or unneeded directories * building 'populationdynamics_0.0-1.tar.gz' * installing *source* package ‘populationdynamics’ ... ** libs *** arch - i386 gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c gillespie.c -o gillespie.o In file included from gillespie.c:28: gillespie.h:3:26: error: gsl/gsl_math.h: No such file or directory gillespie.h:4:29: error: gsl/gsl_randist.h: No such file or directory gillespie.h:5:25: error: gsl/gsl_rng.h: No such file or directory gillespie.h:6:28: error: gsl/gsl_vector.h: No such file or directory gillespie.h:7:32: error: gsl/gsl_statistics.h: No such file or directory gillespie.c: In function ‘gillespie’: gillespie.c:80: error: ‘gsl_rng’ undeclared (first use in this function) gillespie.c:80: error: (Each undeclared identifier is reported only once gillespie.c:80: error: for each function it appears in.) gillespie.c:80: error: ‘rng’ undeclared (first use in this function) gillespie.c:80: warning: implicit declaration of function ‘gsl_rng_alloc’ gillespie.c:80: error: ‘gsl_rng_default’ undeclared (first use in this function) gillespie.c:82: warning: implicit declaration of function ‘gsl_rng_set’ gillespie.c:98: warning: implicit declaration of function ‘calloc’ gillespie.c:98: warning: incompatible implicit declaration of built-in function ‘calloc’ gillespie.c:113: warning: implicit declaration of function ‘gsl_ran_exponential’ gillespie.c:119: warning: implicit declaration of function ‘gsl_rng_uniform’ gillespie.c:129: warning: implicit declaration of function ‘free’ gillespie.c:133: warning: implicit declaration of function ‘gsl_rng_free’ make: *** [gillespie.o] Error 1 ERROR: compilation failed for package ‘populationdynamics’ * removing ‘/Library/Frameworks/R.framework/Versions/2.14/Resources/library/populationdynamics’ Warning message: In install.packages(built_path, repos = NULL, type = "source") : installation of package ‘/var/folders/69/7ztsqtsx4js1m7y_mhcrgmdw0000gn/T//RtmpMlTTfy/populationdynamics_0.0-1.tar.gz’ had non-zero exit status

populationdynamics depends on the gsl libraries. this might help? http://ascend4.org/Binary_installer_for_GSL-1.13_on_Mac_OS_X

On Tue, Feb 14, 2012 at 11:04 AM, noamross < reply@reply.github.com

wrote:

I get an error when I try to run the demo on the wiki, because of the populationdynamicspackage. However, when I try to install it, I get an error as well:


> install_github("populationdynamics", "cboettig")
Installing populationdynamics from cboettig
Installing populationdynamics
* checking for file
'/private/var/folders/69/7ztsqtsx4js1m7y_mhcrgmdw0000gn/T/RtmpMlTTfy/cboettig-populationdynamics-efc1ef7/DESCRIPTION'
... OK
* preparing 'populationdynamics':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'populationdynamics_0.0-1.tar.gz'

* installing *source* package populationdynamics ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386
 -I/usr/local/include    -fPIC  -g -O2 -c gillespie.c -o gillespie.o
In file included from gillespie.c:28:
gillespie.h:3:26: error: gsl/gsl_math.h: No such file or directory
gillespie.h:4:29: error: gsl/gsl_randist.h: No such file or directory
gillespie.h:5:25: error: gsl/gsl_rng.h: No such file or directory
gillespie.h:6:28: error: gsl/gsl_vector.h: No such file or directory
gillespie.h:7:32: error: gsl/gsl_statistics.h: No such file or directory
gillespie.c: In function gillespie:
gillespie.c:80: error: gsl_rng undeclared (first use in this function)
gillespie.c:80: error: (Each undeclared identifier is reported only once
gillespie.c:80: error: for each function it appears in.)
gillespie.c:80: error: rng undeclared (first use in this function)
gillespie.c:80: warning: implicit declaration of function gsl_rng_alloc
gillespie.c:80: error: gsl_rng_default undeclared (first use in this
function)
gillespie.c:82: warning: implicit declaration of function gsl_rng_set
gillespie.c:98: warning: implicit declaration of function calloc
gillespie.c:98: warning: incompatible implicit declaration of built-in
function calloc
gillespie.c:113: warning: implicit declaration of function
gsl_ran_exponential
gillespie.c:119: warning: implicit declaration of function
gsl_rng_uniform
gillespie.c:129: warning: implicit declaration of function free
gillespie.c:133: warning: implicit declaration of function gsl_rng_free
make: *** [gillespie.o] Error 1
ERROR: compilation failed for package populationdynamics
* removing
/Library/Frameworks/R.framework/Versions/2.14/Resources/library/populationdynamics
Warning message:
In install.packages(built_path, repos = NULL, type = "source") :
 installation of package
/var/folders/69/7ztsqtsx4js1m7y_mhcrgmdw0000gn/T//RtmpMlTTfy/populationdynamics_0.0-1.tar.gz
had non-zero exit status

Reply to this email directly or view it on GitHub: https://github.com/cboettig/earlywarning/issues/1

Carl Boettiger UC Davis http://www.carlboettiger.info/

cboettig / earlywarning

Can't run demo in wiki because of populationdynamics package #1