Error when installing latest macs2

[dbrg77]

Hi Tao,

I currently have macs2 20140616 installed, and I noticed that there is a new version 20150731.

So I downloaded the source code from pypi, and tried to install it. However, I got the following error:

$ python setup.py install
running install
running bdist_egg
running egg_info
writing requirements to MACS2.egg-info/requires.txt
writing MACS2.egg-info/PKG-INFO
writing top-level names to MACS2.egg-info/top_level.txt
writing dependency_links to MACS2.egg-info/dependency_links.txt
writing requirements to MACS2.egg-info/requires.txt
writing MACS2.egg-info/PKG-INFO
writing top-level names to MACS2.egg-info/top_level.txt
writing dependency_links to MACS2.egg-info/dependency_links.txt
reading manifest file 'MACS2.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'MANIFEST'
no previously-included directories found matching 'test'
writing manifest file 'MACS2.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
running build_ext
building 'MACS2.Prob' extension
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/homes/xichen/anaconda/lib/python2.7/site-packages/numpy/core/include -I/homes/xichen/anaconda/include/python2.7 -c MACS2/Prob.c -o build/temp.linux-x86_64-2.7/MACS2/Prob.o -w -Ofast
cc1: error: invalid option argument ‘-Ofast’
error: command 'gcc' failed with exit status 1

when I tried to install using pip, similar thing happens:

$ pip install -U MACS2
Collecting MACS2
Downloading MACS2-2.1.0.20150731.tar.gz (1.6MB)
100% |████████████████████████████████| 1.6MB 190kB/s
Requirement already up-to-date: numpy>=1.6 in ./anaconda/lib/python2.7/site-packages (from MACS2)
Installing collected packages: MACS2
Found existing installation: MACS2 2.0.10.20131216
DEPRECATION: Uninstalling a distutils installed project (MACS2) has been deprecated and will be removed in a future version. This is due to the fact that uninstalling a distutils project will only partially uninstall the project.
Uninstalling MACS2-2.0.10.20131216:
Successfully uninstalled MACS2-2.0.10.20131216
Running setup.py install for MACS2
Complete output from command /homes/xichen/anaconda/bin/python -c "import setuptools, tokenize;file='/tmp/pip-build-6Z52HD/MACS2/setup.py';exec(compile(getattr(tokenize, 'open', open)(file).read().replace('\r\n', '\n'), file, 'exec'))" install --record /tmp/pip-ait1FG-record/install-record.txt --single-version-externally-managed --compile:
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/MACS2
copying MACS2/init.py -> build/lib.linux-x86_64-2.7/MACS2
copying MACS2/diffpeak_cmd.py -> build/lib.linux-x86_64-2.7/MACS2
copying MACS2/bdgdiff_cmd.py -> build/lib.linux-x86_64-2.7/MACS2
copying MACS2/cmbreps_cmd.py -> build/lib.linux-x86_64-2.7/MACS2
copying MACS2/refinepeak_cmd.py -> build/lib.linux-x86_64-2.7/MACS2
copying MACS2/OptValidator.py -> build/lib.linux-x86_64-2.7/MACS2
copying MACS2/predictd_cmd.py -> build/lib.linux-x86_64-2.7/MACS2
copying MACS2/filterdup_cmd.py -> build/lib.linux-x86_64-2.7/MACS2
copying MACS2/bdgopt_cmd.py -> build/lib.linux-x86_64-2.7/MACS2
copying MACS2/bdgbroadcall_cmd.py -> build/lib.linux-x86_64-2.7/MACS2
copying MACS2/OutputWriter.py -> build/lib.linux-x86_64-2.7/MACS2
copying MACS2/Constants.py -> build/lib.linux-x86_64-2.7/MACS2
copying MACS2/bdgpeakcall_cmd.py -> build/lib.linux-x86_64-2.7/MACS2
copying MACS2/bdgcmp_cmd.py -> build/lib.linux-x86_64-2.7/MACS2
copying MACS2/pileup_cmd.py -> build/lib.linux-x86_64-2.7/MACS2
copying MACS2/randsample_cmd.py -> build/lib.linux-x86_64-2.7/MACS2
copying MACS2/callpeak_cmd.py -> build/lib.linux-x86_64-2.7/MACS2
creating build/lib.linux-x86_64-2.7/MACS2/IO
copying MACS2/IO/init.py -> build/lib.linux-x86_64-2.7/MACS2/IO
copying MACS2/IO/test_threading.py -> build/lib.linux-x86_64-2.7/MACS2/IO
copying MACS2/IO/test_processing.py -> build/lib.linux-x86_64-2.7/MACS2/IO
copying MACS2/IO/BinKeeper.py -> build/lib.linux-x86_64-2.7/MACS2/IO
running build_ext
building 'MACS2.Prob' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/MACS2
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/homes/xichen/anaconda/lib/python2.7/site-packages/numpy/core/include -I/homes/xichen/anaconda/include/python2.7 -c MACS2/Prob.c -o build/temp.linux-x86_64-2.7/MACS2/Prob.o -w -Ofast
cc1: error: invalid option argument ‘-Ofast’
error: command 'gcc' failed with exit status 1

----------------------------------------

Rolling back uninstall of MACS2

Any idea how to solve this problem? I vaguely remember there was somebody has similar issue with -Ofast, but I could not locate the solution.

Thanks.

Xi

[taoliu]

It seems your GCC doesn't have '-Ofast' option. Check the issue #75. #75

[lparsons]

I've run into this as well, and was wondering about the idea of adjust the compiler options on the fly? Or maybe just use the more compatible -O3 flag? Otherwise, a number of users will end up having to patch during installs (e.g. on CentOS6 systems).

Perhaps something like this? http://stackoverflow.com/questions/724664/python-distutils-how-to-get-a-compiler-that-is-going-to-be-used

[taoliu]

@lparsons Thanks for the comments! Could you check if the recent commit cf84fb8 works on older GCC? I simply replaced '-Ofast' with equivalent '-O3' and '-ffast-math'.

[GildasLepennetier]

Hi there.
For some reasons, I had some error during installation. No idea why, and cannot solve it. I decided to install it using docker. In case some people are facing the same problem, I will share here the steps (Using Linux Mint, based on Ubuntu):

1. install docker
   sudo apt install docker
   -> create "Dockerfile" text file
   -> paste in the file:

FROM python:2.7.15-jessie
RUN pip install numpy scipy # Install any needed packages
RUN pip install MACS2 # Install macs2
CMD /bin/bash # enty point`

2. build the image
   docker build -t lepennetier/macs2:2.1.1.20160309 .

3. start the docker container, with a mounted volume pointing where your data is stored (here: $HOME will be available in mnt/ directory)
   docker run -it --rm -v $HOME:/mnt lepennetier/macs2:2.1.1.20160309
   From here, you will have access to macs2 program, try it using macs2 -h

Following are the errors I obtain while trying to install on my broken? system:
I run the command
sudo python setup_w_cython.py install

The error was:

x86_64-linux-gnu-gcc: error: MACS2/IO/Parser.c: No such file or directory
x86_64-linux-gnu-gcc: fatal error: no input files
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

Can not get it from pip neither:

sudo -H pip install MACS2
Collecting MACS2
Using cached https://files.pythonhosted.org/packages/9f/<...>.tar.gz
Complete output from command python setup.py egg_info:
CRITICAL: Python version must be 2.7!
----------------------------------------
Command python setup.py egg_info failed with error code 1 in /tmp/pip-install-tdpab4p1/MACS2/

python --version
Python 2.7.12