TreeMix compilation issues - GSL

[jorhodes]

Hello,

I am having issues compiling TreeMix on my system.  It seems to be related to GSL.

Mac OS X 10.9.3

Boost 1.55 (present in /usr/local/boost_1_55_0)

GSL installed (1.16 present in /usr/local/gsl-1.16)

TreeMix 1.12

It fails when I try to configure TreeMix:

$ ./configure 

"checking for cblas_dgemm in -lgslcblas... no

configure: error: could not find GSL BLAS"

Any ideas?

Many thanks

[Vikram Chhatre]

Check the configure script for where it expects the gsl location to be.  

V

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[jorhodes]

Thanks for your reply.  I did try $ ./configure CPPFLAGS=-I/usr/local/gsl-1.16/ in case it was a nonstandard directory.  Turns out, the problem was actually the need for command line tools to be installed.

On Wednesday, July 2, 2014 4:01:08 PM UTC+1, Vikram Chhatre wrote:

Check the configure script for where it expects the gsl location to be.  

V

On Wed, Jul 2, 2014 at 10:57 AM, jorhodes <johanna...@gmail.com> wrote:

Hello,

I am having issues compiling TreeMix on my system.  It seems to be related to GSL.

Mac OS X 10.9.3

Boost 1.55 (present in /usr/local/boost_1_55_0)

GSL installed (1.16 present in /usr/local/gsl-1.16)

TreeMix 1.12

It fails when I try to configure TreeMix:

$ ./configure 

"checking for cblas_dgemm in -lgslcblas... no

configure: error: could not find GSL BLAS"

Any ideas?

Many thanks

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[Vikram Chhatre]

Ah yes, you need that on OSX.

V

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[Libby]

Hi,

I am having exactly the same issue - same error message on OS 10.9.5. I have gsl and boost installed through MacPorts and have verified that Xcode and command line tools are correctly installed. What else can I try to fix this?

Thanks in advance for any suggestions.

- Libby

[Joseph Pickrell]

Hi Libby,

If MacPorts installs to /opt/local (which is the default on my
machine, so possibly yours as well), you can try:

./configure LDFLAGS=-L/opt/local/lib CPPFLAGS=-I/opt/local/include

Best,

Joe

[Libby Beckman]

Hi Joe,

Thanks so much! That worked perfectly! I can't wait to get started analyzing my data now.

- Libby

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Museum of Southwestern Biology, Department of Biology
University of New Mexico

[Kimberly McManus]

Hi,

I had the same error as Libby and running ./configure LDFLAGS=-L/opt/local/lib CPPFLAGS=-I/opt/local/include appears to allow the configure script to run correctly. I am running OSX 10.8.5. I am using macports and downloaded gsl and boost. However when I run "make", I now get the following error:

"make all-recursive
Making all in src
g++ -DHAVE_CONFIG_H -I. -I.. -I/opt/local/include -I/opt/local/include -g -O2 -MT TreeMix.o -MD -MP -MF .deps/TreeMix.Tpo -c -o TreeMix.o TreeMix.cpp
In file included from /usr/local/lib/gcc/x86_64-apple-darwin14.0.0/4.9.2/include/stdint.h:9:0,
from /opt/local/include/boost/cstdint.hpp:60,
from /opt/local/include/boost/integer_fwd.hpp:17,
from /opt/local/include/boost/integer/static_log2.hpp:19,
from /opt/local/include/boost/functional/hash/detail/hash_float.hpp:17,
from /opt/local/include/boost/functional/hash/hash.hpp:21,
from /opt/local/include/boost/functional/hash.hpp:6,
from /opt/local/include/boost/unordered/unordered_set.hpp:21,
from /opt/local/include/boost/unordered_set.hpp:17,
from /opt/local/include/boost/graph/adjacency_list.hpp:21,
from Settings.hpp:44,
from TreeMix.cpp:8:
/usr/local/lib/gcc/x86_64-apple-darwin14.0.0/4.9.2/include-fixed/stdint.h:27:32: fatal error: sys/_types/_int8_t.h: No such file or directory
#include <sys/_types/_int8_t.h>
^
compilation terminated.
make[2]: *** [TreeMix.o] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2"

Do you know what could cause this error?

Thanks for your help!

Cheers,
Kimberly

[Joseph Pickrell]

Hi Kimberly, 

Thanks for this. I've never seen this before, but it looks like a Boost error. What version of Boost are you using (this will be one of the last lines in /opt/local/include/boost/version.hpp)?

Joe

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[Kimberly McManus]

I just downloaded boost/gsl/macports this week. It says the boost version is:

"boost @1.57.0_0+no_single+no_static+python27 (active)"

The version.hpp also says "#define BOOST_VERSION 105700, #define BOOST_LIB_VERSION "1_57""

Thanks!
Kimberly

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[Joseph Pickrell]

Hi Kimberly, 

Thanks. What happens if you run:

locate _int8_t.h

at the command line?

Best, 

Joe

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[Kimberly McManus]

Hi Joe,

locate _int8_t.h outputs

"/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/System/Library/Frameworks/Kernel.framework/Versions/A/Headers/sys/_types/_int8_t.h
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/sys/_types/_int8_t.h
/Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS7.1.sdk/usr/include/sys/_types/_int8_t.h
/Applications/Xcode.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator7.1.sdk/usr/include/sys/_types/_int8_t.h"

Thanks!
Kimberly

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[Kimberly McManus]

Hey Joe,

I never figured out the problem, but I successfully installed it on another device. Thanks for your help!

Cheers,
Kimberly