'gcc' failed during pandas build on AWS Elastic Beanstalk

19
votes

Getting the following error when trying to install Pandas (0.16.0), which is in my requirements.txt file, on AWS Elastic Beanstalk EC2 instance:

  building 'pandas.msgpack' extension

  gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D__LITTLE_ENDIAN__=1 -Ipandas/src/klib -Ipandas/src -I/opt/python/run/venv/local/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c pandas/msgpack.cpp -o build/temp.linux-x86_64-2.7/pandas/msgpack.o

  gcc: error trying to exec 'cc1plus': execvp: No such file or directory

  error: command 'gcc' failed with exit status 1

I'm running on 64bit Amazon Linux 2015.03 v1.3.0 running Python 2.7 and previously ran into this same error on a t1.micro instance, which was resolved when I change to a m3.medium, but I'm running an m3.xlarge so can't be a memory issue.

I have also ensured that gcc is installed as a package in .ebextensions/00_gcc.config:

packages:
   yum:
      gcc: []
      gcc-c++: []
5
pythonamazon-web-servicespandasamazon-ec2amazon-elastic-beanstalk
Had this issue for a few days now. Rebuilding the environment and then activating x-ray and enhanced health/logging resolved this issue. Although i have no idea why there is a connection. – Andrey Bulezyuk

5 Answers

20
votes

For pandas being compiled on Elastic Beanstalk, make sure to have both packages: gcc-c++ and python-devel

packages:
   yum:
      gcc-c++: []
      python-devel: []
-1
votes

Install python-dev

sudo apt-get install python-dev

For python3

sudo apt-get install python3-dev
-1
votes

on ec2 instances if you run into gcc error; try this

  1. sudo yum install gcc python-setuptools python-devel postgresql-devel

  2. sudo su -

  3. sudo pip install

-1
votes

I had to upgrade amazon's EC2 pip. You can do this by editing the .config file in .ebextensions:

sh commands: 00_update_pip: command: "/opt/python/run/venv/bin/pip install --upgrade pip"

-1
votes

I solved this issue by ssh'ing in to the EBS machine and updating pip

pip install -U pip