Building R (cran) + rpy2 on ubuntu -> libRblas.so not found -


i trying build r (tried 2.14.2 , 2.15) , rpy2 (2.2.6, python 2.7.1) on ubuntu (11.04, natty narwhal), deploy custom directory (in following called /home/me/lib/r), since not have root access, need newer version available on server.

details of build etc further down, when running tests of rpy2, following error:

/home/me/lib/pythonlib/lib/python/rpy2/rinterface/__init__.py in <module>() ---> 87 rpy2.rinterface._rinterface import * importerror: librblas.so: cannot open shared object file: no such file or directory warning: failure executing file: <experiments/arrangement/test_smacof_arrange.py>

i sure calling right rpy2 module (my custom built one) has been built against custom built r version. doing following:

  1. i first build r-base on ubuntu

    wget http://cran.r-project.org/bin/linux/ubuntu/natty/r-base_2.14.2.orig.tar.gz # untar , go directory  # enable-r-shblib flag needed rpy2 linking, enable-blas-shlib included # because hoped solve problem, doesnt change ./configure --enable-r-shlib --enable-blas-shlib --prefix=/home/me/lib/r make make install

  2. i build rpy2 against r build

    wget http://pypi.python.org/packages/source/r/rpy2/rpy2-2.2.6.tar.gz # untar , go directory  # build rpy2, providing r-home-lib , r-home flags, , deploy custom dir python setup.py build --r-home /home/me/lib/r --r-home-lib /home/me/lib/r/lib64/r/lib install --home /home/me/lib/pythonlib

    i have adapted pythonpath find modules in /home/me/lib/pythonlib, problem isn't there. python build returns correct configuration (note rblas appears here!)

    configuration r library: include_dirs: ('/home/me/lib/r/lib64/r/include',) libraries: ('r', 'rblas', 'rlapack') library_dirs: ('/home/me/lib/r/lib64/r/lib',) extra_link_args: ()

i have tried track down error, no end. /home/me/lib/r/lib64/r/lib contains librblas.so, there 1 thing seems strange however, librblas.so not linked correctly libr.so, not sure wether causes error, nor know how fix it.

>> ldd -d libr.so  linux-vdso.so.1 =>  (0x00007fffcec58000) librblas.so => not found libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3 (0x00007fe63d21d000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fe63cf97000) ...

any appreciated!

for others running issue, able solve making sure add r libraries library path in bashrc:

export ld_library_path="r-install-location/lib65/r/lib:$ld_library_path"

Comments

Post a Comment

Popular posts from this blog

java - Play! framework 2.0: How to display multiple image? -

i need display gallery of photos. here template: @(photos: list[photo]) @title = { <bold>gallery</bold> } @main(title,"photo"){ <ul class="thumbnails"> @for(photo <- photos) { <li class="span3"> <a href="#" class="thumbnail"> <img src="@photo.path" alt=""> </a> </li> } </ul> } and here controller method: public static result getphotos() { return ok(views.html.photo.gallery.render(photo.get())); } and here photo bean : @entity public class photo extends model { @id public long id; @required public string label; public string path; public photo(string path, string label) { this.path = path; this.label = label; } private static finder<long, photo> find = new finder<long, photo>( long.class, photo.class); public static list<phot...
Read more

gmail - Is there any documentation for read-only access to the Google Contacts API? -

i want read-only access user's google contacts. there stackoverflow member wanted this, , received following answer : yes, there is, use https://www.googleapis.com/auth/contacts.readonly scope , "view contacts". this exchange reference read-only access google contacts can find using google. simply using access token obtained attempt read usual google contacts api (i.e. https://www.google.com/m8/feeds ) fails insufficient permissions. similarly, using google contacts api on new target fails 404 errors (for example https://www.googleapis.com/auth/contacts.readonly/default/full ). is there documentation anywhere on how use api, or permissible way access google contacts api full read-write access?
Read more

php - Controller/JToolBar not working in Joomla 2.5 -

relevant code: jtoolbarhelper::custom('savecategories', 'save', '', 'save', false, false); ... <input type="hidden" name="controller" value="easyblogcontroller"> according can dig docs , own previous questions, should call savecategories() function in easyblogcontroller . i've tried setting value easyblog , easyblog.php (file name) current easyblogcontroller (class name). clicking on save button refreshes page. not redirect, echo or var_dump test code put in savecategories() function. var_dump ing jrequest::getvar('controller') , 'task' return correct values. creating controller object , using $controller->execute('task'); works. the values going depend on location of controller trying call, , have couple options here. typically there controller in base folder of component (likely components/com_easyblog) in file called controller.php , class name inside ...
Read more