I'm running the following commands in python:
from rpy2.robjects.packages import importr
importr( 'ggplot2' )
This works fine in python-2.7.6 and rpy2-2.8.3. However it gives the following error when run on python-2.7.8 and rpy2-2.8.5 :
/usr/local/lib/python2.7/dist-packages/rpy2/rinterface/__init__.py:186: RRuntimeWarning: Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/usr/local/lib/R/site-library/Rcpp/libs/Rcpp.so':
/usr/local/lib/R/site-library/Rcpp/libs/Rcpp.so: undefined symbol: R_ClassSymbol
warnings.warn(x, RRuntimeWarning)
Segmentation fault (core dumped)
rpy2 is a package which provide access to R when you are using python. So firstly make sure that you enabled R-shared libs when you compiles you R as follows:
./configure --prefix=* --with-x=no --enable-R-shlib=yes
make sure you have specified the following environment variable before you distribute your rpy2 package:
export C_INCLUDE_PATH=/path/to/R/lib64/R/include
Last but not least, only those packages installed when all of this requirements are satisfied can be rightly imported in python by importr. And if not, you may need to reinstall the R packages.
Related
I am installing Tensorflow. I encountered the following problem:
I was installing Tensorflow from Source and I am following the Tensorflow website (https://www.tensorflow.org/install/source)
I had earlier installed Bazel 3.0.0 (the latest version) but got a similar error. Upon looking at other answers I figured out this error has something to do with the version of Bazel. Hence I uninstalled Bazel 3.0.0 and installed Bazel 0.27.1. But upon typing the following command(bazel build //tensorflow/tools/pip_package:build_pip_package) in the terminal, I am getting the following error:
WARNING: The following rc files are no longer being read, please transfer their contents or import their path into one of the standard rc files:
/home/aviraj/tensorflow/tools/bazel.rc
Starting local Bazel server and connecting to it...
ERROR: /home/aviraj/tensorflow/WORKSPACE:3:1: name 'http_archive' is not defined
ERROR: Error evaluating WORKSPACE file
ERROR: error loading package '': Encountered error while reading extension file 'closure/defs.bzl': no such package '#io_bazel_rules_closure//closure': error loading package 'external': Could not load //external package
ERROR: error loading package '': Encountered error while reading extension file 'closure/defs.bzl': no such package '#io_bazel_rules_closure//closure': error loading package 'external': Could not load //external package
INFO: Elapsed time: 2.023s
INFO: 0 processes.
FAILED: Build did NOT complete successfully (0 packages loaded)
Any help would be much appreciated. Thanks
Starting with version 0.20.0, http_archive native rule has been deprecated, it has to be loaded from: #bazel_tools//tools/build_defs/repo:http.bzl. I.e. you need to add the following (unless you have a customized version) in WORKSPACE or bzl files using it:
load("#bazel_tools//tools/build_defs/repo:http.bzl", "http_archive")
I'm trying to use the R (Version 3.4.3) package MICE in Python 3.6.5 with rpy2.
This is the code I use:
import os
os.environ['R_HOME'] = 'C:/Program Files/R/R-3.4.3'
os.environ['R_USER'] = 'C:/Users/username/Anaconda3/Lib/site-packages/rpy2'
import rpy2.robjects as ro
from rpy2.robjects.packages import importr
mice = importr('mice', lib_loc ='C:\Program Files\R\R-3.4.3\library')
When I execute this, my Jupyter notebook dies. In the terminal I get the error message:
Error: package or namespace load failed for 'stats' in inDL(x, as.logical(local), as.logical(now), ...):
unable to load shared object 'C:/Program Files/R/R-3.4.3/library/stats/libs/x64/stats.dll':
LoadLibrary failure: The specified module could not be found.
During startup - Warning message:
package 'stats' in options("defaultPackages") was not found
Error: '\P' is an unrecognized escape in character string starting ""C:\P"
But I do have the package stats installed and the file 'C:/Program Files/R/R-3.4.3/library/stats/libs/x64/stats.dll' exists.
Does anybody know a solution for this problem?
I installed the package mice in RStudio. I made sure that all my installed R libraries are in the directory C:/Program Files/R/R-3.4.3/library so that dependencies of mice are found in the same folder. For this I just copied all the packages installed in another folder to that one (I hope that's not a problem?)
I'm trying to run a script that requires the datasets python package. I've tried installing this unsuccessfully using pip by calling:
pip install datasets
I know this hasn't worked because when I run the script I get the message:
Traceback (most recent call last):
File "lda.py", line 2, in <module>
import lda
File "/Users/deepthought/lda.py", line 3, in <module>
import datasets
ImportError: No module named datasets
I've installed python via homebrew.
When I run pip install datasets I get the error:
Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/ch/84cpkwc52zx0rsh4k5v4_7h40000gn/T/pip-build-gZWyT3/datasets/
I'm fairly new to scripting python or going under the hood of an OS X, so there's a risk I've missed something elementary.
I've been researching & trying to overcome this for about a week now including looking at similar questions on stackoverflow.com and haven't gotten past this stage for the duration. One of the tutorials I was working through told me to edit ~/.profile
This has been left like so:
# The orginal version is saved in .profile.pysave
#PATH="/Library/Frameworks/Python.framework/Versions/3.5/bin:${PATH}"
#export PATH
export PATH=/usr/local/bin:/usr/local/sbin:$PATH
/etc/paths contains:
/usr/local/bin
/usr/bin
/bin
/usr/sbin
/sbin
I'm running OS X El Capitan - 10.11.5 (15F34)
Python 2.7.11
Brew doctor flagged multiple items, but I've no idea whether it is worth fixing none/all of them:
Warning: Your XQuartz (2.7.7) is outdated
Please install XQuartz 2.7.9:
https://xquartz.macosforge.org
Warning: Python is installed at /Library/Frameworks/Python.framework
Homebrew only supports building against the System-provided Python or a
brewed Python. In particular, Pythons installed to /Library can interfere
with other software installs.
Warning: Unbrewed dylibs were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected dylibs:
/usr/local/lib/libtcl8.6.dylib
/usr/local/lib/libtk8.6.dylib
Warning: Unbrewed header files were found in /usr/local/include.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected header files:
/usr/local/include/fakemysql.h
/usr/local/include/fakepq.h
/usr/local/include/fakesql.h
/usr/local/include/itcl.h
/usr/local/include/itcl2TclOO.h
/usr/local/include/itclDecls.h
/usr/local/include/itclInt.h
/usr/local/include/itclIntDecls.h
/usr/local/include/itclMigrate2TclCore.h
/usr/local/include/itclTclIntStubsFcn.h
/usr/local/include/mysqlStubs.h
/usr/local/include/node/ares.h
/usr/local/include/node/ares_version.h
/usr/local/include/node/nameser.h
/usr/local/include/node/node.h
/usr/local/include/node/node_buffer.h
/usr/local/include/node/node_internals.h
/usr/local/include/node/node_object_wrap.h
/usr/local/include/node/node_version.h
/usr/local/include/node/openssl/opensslconf.h
/usr/local/include/node/uv-private/ngx-queue.h
/usr/local/include/node/uv-private/stdint-msvc2008.h
/usr/local/include/node/uv-private/tree.h
/usr/local/include/node/uv-private/uv-bsd.h
/usr/local/include/node/uv-private/uv-darwin.h
/usr/local/include/node/uv-private/uv-linux.h
/usr/local/include/node/uv-private/uv-sunos.h
/usr/local/include/node/uv-private/uv-unix.h
/usr/local/include/node/uv-private/uv-win.h
/usr/local/include/node/uv.h
/usr/local/include/node/v8-debug.h
/usr/local/include/node/v8-preparser.h
/usr/local/include/node/v8-profiler.h
/usr/local/include/node/v8-testing.h
/usr/local/include/node/v8.h
/usr/local/include/node/v8stdint.h
/usr/local/include/node/zconf.h
/usr/local/include/node/zlib.h
/usr/local/include/odbcStubs.h
/usr/local/include/pqStubs.h
/usr/local/include/tcl.h
/usr/local/include/tclDecls.h
/usr/local/include/tclOO.h
/usr/local/include/tclOODecls.h
/usr/local/include/tclPlatDecls.h
/usr/local/include/tclThread.h
/usr/local/include/tclTomMath.h
/usr/local/include/tclTomMathDecls.h
/usr/local/include/tdbc.h
/usr/local/include/tdbcDecls.h
/usr/local/include/tdbcInt.h
/usr/local/include/tk.h
/usr/local/include/tkDecls.h
/usr/local/include/tkPlatDecls.h
Warning: Unbrewed .pc files were found in /usr/local/lib/pkgconfig.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected .pc files:
/usr/local/lib/pkgconfig/tcl.pc
/usr/local/lib/pkgconfig/tk.pc
Warning: Unbrewed static libraries were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected static libraries:
/usr/local/lib/libtclstub8.6.a
/usr/local/lib/libtkstub8.6.a
Warning: You have unlinked kegs in your Cellar
Leaving kegs unlinked can lead to build-trouble and cause brews that depend on
those kegs to fail to run properly once built. Run `brew link` on these:
git
python3
Warning: Broken symlinks were found. Remove them with `brew prune`:
/usr/local/bin/github
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Warning: Your Homebrew is outdated.
You haven't updated for at least 24 hours. This is a long time in brewland!
To update Homebrew, run `brew update`.
How do I make progress in diagnosing the issue with the installation of the datasets package?
Update
Here is the script I'm trying to run:
import sys
egg_path = '/usr/local/lib/python2.7/site-packages/datasets-0.0.9-py2.7.egg'
sys.path.append(egg_path)
import numpy as np
import lda
import datasets
X = lda.datasets.load_reuters()
vocab = lda.datasets.load_reuters_vocab()
titles = lda.datasets.load_reuters_titles()
X.shape
(395, 4258)
X.sum()
84010
model = lda.LDA(n_topics=20, n_iter=1500, random_state=1)
model.fit(X) # model.fit_transform(X) is also available
topic_word = model.topic_word_ # model.components_ also works
n_top_words = 8
for i, topic_dist in enumerate(topic_word):
topic_words = np.array(vocab)[np.argsort(topic_dist)][:-(n_top_words+1):-1]
print('Topic {}: {}'.format(i, ' '.join(topic_words)))
Using pip install datasets I was also not able to properly install this package. It seems like there is a bug in this particular package.
The DESCRIBE.rst file is simply missing. To fix this just download the plain package from PyPi. https://pypi.python.org/pypi/datasets/0.0.9
Then adjust the setup.py file (remove the description).
Afterwards you need to install using python setup.py install. Don't forget to add the installed package to your Python path!
To do so, I would recommend that you add the following to your script.
import sys
egg_path = '__MODULE_PATH__/datasets-0.0.9-py3.5.egg'
sys.path.append(egg_path)
import datasets
Otherwise, you can also add your module using:
export PATH=__MODULE_PATH__:$PATH
Alternatively, you could also simply pull the source code from the Github repository and just include it in your project. https://github.com/realtimeweb/datasets
Hope this was kind of helpful to your problem. If you got any further questions just let me know.
I just hit the same issue on a rapsberry pi, just found out this had been fixed but the error comes from the lack of ram to extract properly the package.
You can fix this by disabling the creation of a cache dir in ram adding the parameter
--no-cache-dir
for example
pip2 install --user --no-cache-dir datasets
I have compiled scip with:
$ IPOPT=true make SHARED=true scipoptlib
It has compiled successfully and I run python setup.py install of the python interface.
However, when I run from pyscipopt.scip import Model in Python, I get the following error message:
ImportError: scip-3.2.1/interfaces/python/lib/libscipopt.so: undefined symbol: _ZTIN5Ipopt7JournalE
You need to adapt the setup.py to also include Ipopt as library to link to.
It's close to the end of the file and is called libraries in the definition of the Cython extension.
To load matplotlib on cygwin, I have:
Loaded pre-requisites using cygwin 64-bit setup: pkg-config, freetype2, libfreetype-devel, libpng-devel, gtk2.0, libgtk2.0-devel
Downloaded the matplotlib tar file (http://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-1.3.1/matplotlib-1.3.1.tar.gz) and changed the source code to get around the "_tri" error as advised here:
matplotlib error while installing pyspeckit
Then built and installed matplotlib:
$ python setup.py build
$ python setup.py install
And am down to what looks like a matplotlib backend error. Does anyone know how to get around this:
/usr/lib/python2.7/site-packages/gtk-2.0/gtk/init.py:57: GtkWarning: could not open display
...
cursors.MOVE : gdk.Cursor(gdk.FLEUR),
et n RuntimeError: could not create GdkCursor object
EDIT: I just finally got it and matplotlib is finally working on cygwin. To do this, I did:
From cygwin setup, loaded the X-Server tools:
xorg-server xinit
From cygwin setup, I also loaded these so that use telnet or ssh connections to run remote X clients:
inetutils openssh
I set my display:
DISPLAY=":0.0"
export DISPLAY
From the cygwin shell, I did:
$ startxwin
Then I ran my python scripts which use matplotlib in the X-window
I had an issue with "python setup.py build" not finding the ft2build.h which comes from the the freetype2 package. I installed the freetype2 development package and I can find it in /usr/include/freetype2/ft2build.h but the error is still there.
After digging into the setupext.py at the function check_include_file(include_dirs, filename, package), I noticed that the package="freetype2" was not concatenated into to the search path. Hence it could not find "/usr/include/ft2build.h" when it should be "/usr/include/freetype2/ft2build.h
Fixing this line #134
if not has_include_file(include_dirs, "%s/%s"%(package,filename)):