xgboost installation issue with anaconda

Question

I am using Anaconda. I first switched to Python2 (Version 2.7.11).

python -V
Python 2.7.11 :: Continuum Analytics, Inc.

I used the following command to install xgboost in anaconda.

conda install -c https://conda.anaconda.org/akode xgboost

I then checked that xgboost is installed.

conda list
xgboost                   0.3                      py27_0    akode

I run python in terminal, import xgboost and got the following errors.

import xgboost as xgb

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "//anaconda/envs/wen2/lib/python2.7/site-packages/xgboost.py", line 82, in <module>
    xglib = load_xglib()
  File "//anaconda/envs/wen2/lib/python2.7/site-packages/xgboost.py", line 59, in load_xglib
    lib = ctypes.cdll.LoadLibrary(lib_path[0])
  File "//anaconda/envs/wen2/lib/python2.7/ctypes/__init__.py", line 443, in LoadLibrary
    return self._dlltype(name)
  File "//anaconda/envs/wen2/lib/python2.7/ctypes/__init__.py", line 365, in __init__
    self._handle = _dlopen(self._name, mode)
OSError: dlopen(//anaconda/envs/wen2/lib/python2.7/site-packages/libxgboostwrapper.so, 6): Library not loaded: @rpath/./libgomp.1.dylib
  Referenced from: //anaconda/envs/wen2/lib/python2.7/site-packages/libxgboostwrapper.so
  Reason: image not found

I have no idea what to do next.

Solution 1

The package image you download is corrupt. What you should do :

First remove your xgboost package with (in the terminal) :

conda remove xgboost

Then reinstall with an other package at https://anaconda.org/aterrel/xgboost So just write :

conda install py-xgboost

Then you can check the installation in the python console :

import xgboost

It should be ok.

Solution 2

I had the same error. I completely uninstalled xgboost by pip unistall. then installed it back by:

conda install -c bioconda xgboost=0.6a2

This seems to solve the problem

Solution 3

You first need to build the library through "make", then you can install using anaconda prompt.

First follow the official guide with the following procedure (in Git Bash on Windows):

git clone --recursive https://github.com/dmlc/xgboost
git submodule init
git submodule update

install TDM-GCC here

alias make='mingw32-make'
cp make/mingw64.mk config.mk; make -j4

Last, do the following using anaconda prompt:

cd xgboost\python-package  
python setup.py install 

Also refer to these great resources:

Official Guide

Installing Xgboost on Windows

Installing XGBoost For Anaconda on Windows

Solution 4

Did you try using pip?
source activate yourenvironment
pip install xgboost

Solution 5

Library not loaded: @rpath/./libgomp.1.dylib

This is the key.

In my case, it is " Library not loaded: /usr/local/opt/gcc/lib/gcc/6/libgomp.1.dylib"

I check my path "/usr/local/opt/gcc/lib/gcc" and there is only a folder named 7 there , no 6.
So i use "sudo find / -name libgomp.1.dylib" to locate all the gcc version i have installed, with I found that there is a version 6 in another location.
Then I create a folder named 6 under '/usr/local/opt/gcc/lib/gcc' and copy those gcc 6 files in there . Finally , "import xgboost" works with no error .

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Comments

[avloss]

looks like that would install xgboost which is out of date, along with sklearn version 0.16.1 (out of date)

[Taposh DuttaRoy]

This did not work for me. My python version is 3.5.2 and the error I get is : bash-4.3$ python -V Python 3.5.2 :: Anaconda 4.2.0 (x86_64) (/Users/xxx/anaconda) bash-4.3$ conda install -c aterrel xgboost Fetching package metadata ......... Solving package specifications: .... UnsatisfiableError: The following specifications were found to be in conflict: - python 3.5* - xgboost Use "conda info <package>" to see the dependencies for each package.

[user1700890]

Thank you, your suggestion worked for me. Do you know what bioconda in your command means?

[Adrien Forbu]

Ok what you should do now is just conda install py-xgboost as 0.4.0 is an old version of xgboost