HTSeq install

fatakias · 04-06-2012, 07:27 AM

Dear HTSeq expert(s)

I am installing HTSeq as root user on OS: Mac OS X (snow leopard).
I downloaded the tarbal from

http://pypi.python.org/pypi/HTSeq

Here is the output of the install and build command:

Code:

sh-3.2# ./clean
sh-3.2# ./build_it
swig -Wall -c++ -python StepVector.i 
mv StepVector.py ../HTSeq
cython HTSeq/_HTSeq.pyx -o _HTSeq.c
make: cython: No such file or directory
make: *** [_HTSeq.c] Error 1
Could not import 'setuptools', falling back to 'distutils'.
running build
running build_py
creating build
creating build/lib.macosx-10.4-x86_64-2.7
creating build/lib.macosx-10.4-x86_64-2.7/HTSeq
copying HTSeq/__init__.py -> build/lib.macosx-10.4-x86_64-2.7/HTSeq
copying HTSeq/_HTSeq_internal.py -> build/lib.macosx-10.4-x86_64-2.7/HTSeq
copying HTSeq/StepVector.py -> build/lib.macosx-10.4-x86_64-2.7/HTSeq
copying HTSeq/_version.py -> build/lib.macosx-10.4-x86_64-2.7/HTSeq
creating build/lib.macosx-10.4-x86_64-2.7/HTSeq/scripts
copying HTSeq/scripts/__init__.py -> build/lib.macosx-10.4-x86_64-2.7/HTSeq/scripts
copying HTSeq/scripts/qa.py -> build/lib.macosx-10.4-x86_64-2.7/HTSeq/scripts
copying HTSeq/scripts/count.py -> build/lib.macosx-10.4-x86_64-2.7/HTSeq/scripts
running build_ext
building 'HTSeq._HTSeq' extension
creating build/temp.macosx-10.4-x86_64-2.7
creating build/temp.macosx-10.4-x86_64-2.7/src
gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c src/_HTSeq.c -o build/temp.macosx-10.4-x86_64-2.7/src/_HTSeq.o -w
gcc: error: src/_HTSeq.c: No such file or directory
gcc: fatal error: no input files
compilation terminated.
error: command 'gcc' failed with exit status 1

Can you please help sort the problem. What is "setuptools" seeking or how does one run that first.
Thanks in advance
Best,
sarosh

Simon Anders · 04-06-2012, 03:15 PM

You are not supposed to run './build_it'. Rather, install HTSeq as you would install any other Python package, by running 'python setup.py install'. And read the installation instructions, please.

ngsseq · 04-07-2012, 12:53 AM

Hi sarosh,

I installed HTSeq on Lion a few days ago. I got the same error message. I searched around and found a solution below:

on the command line,
add “export CC=gcc" into ~/.bash_profile,
then “source ~/.bash_profile".

I wish it would help.

Regards,
ngsseq

yifangt · 04-30-2012, 10:11 PM

Hi Simon!
I met similar problem when I tried to install HTSeq-0.5.3p3. Read the other posts on similar problem in this forum and google, not direct clear solution yet.

Code:

Could not import 'setuptools', falling back to 'distutils'.

But the rest went fine. Modified the .bashrc file as suggested by ngsseq (which seems for Mac OS, but gave it shot just in case!) still did not work. My python version is 2.7.2+ Any news for this Bug? Thanks!

yifangt · 04-30-2012, 11:43 PM

Just in case anyone met the same problem. First updated my python to python3.2, still not working. Should have paid attention on the instruction (>=2.5 PYTHON <3.0). After a couple of try found out my problem is related to setuptools and python 3.2.
1) I had setuptools3 instead of setuptools. Decided to have both.
After this, building from the source code went well, but met problem with

Code:

python setup.py install

on line 12 of setup.py. Thought of the python version.
2) symbolic link my python to /usr/bin/python2.7.2 instead of /usr/bin/python3.2. Worked!
And when I came back also found new version was released in another post, which does not need setuptools.
Good luck!

Simon Anders · 05-01-2012, 12:42 AM

You don't need setuptools, distutils works just fine. (This is what a "fallback" means.)

fatakias · 05-01-2012, 07:06 AM

Hello, now I get a different error message pertaining to gcc. I did manage to install numpy and scipy using a super_pack script for my 64 bin MacOS 10.6. Then tried to get HTSeq going ... compiler issues linger. Can you please suggest a fix. Thank you,
Best,
sarosh

Code:

sh-3.2# cd HTSeq-0.5.3p3
sh-3.2# python setup.py install
running install
running bdist_egg
running egg_info
writing HTSeq.egg-info/PKG-INFO
writing top-level names to HTSeq.egg-info/top_level.txt
writing dependency_links to HTSeq.egg-info/dependency_links.txt
reading manifest file 'HTSeq.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
no previously-included directories found matching 'example_data'
no previously-included directories found matching 'test'
warning: no previously-included files found matching 'todo.txt'
writing manifest file 'HTSeq.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-10.4-x86_64/egg
running install_lib
running build_py
running build_ext
building 'HTSeq._HTSeq' extension
gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/lib/python2.7/site-packages/numpy-1.7.0.dev_3cb783e_20120427-py2.7-macosx-10.7-x86_64.egg/numpy/core/include -I/usr/local/include/python2.7 -c src/_HTSeq.c -o build/temp.macosx-10.4-x86_64-2.7/src/_HTSeq.o -w
gcc: error: src/_HTSeq.c: No such file or directory
gcc: fatal error: no input files
compilation terminated.
error: command 'gcc' failed with exit status 1

fatakias · 05-01-2012, 08:26 AM

Continued from above post - after a clean up .. Additional details provided. Can someone please suggest a fix for HTSeq install. Thanks,
Best,
sarosh

Code:

sh-3.2# sh clean

sh-3.2# python setup.py install
running install
running bdist_egg
running egg_info
writing HTSeq.egg-info/PKG-INFO
writing top-level names to HTSeq.egg-info/top_level.txt
writing dependency_links to HTSeq.egg-info/dependency_links.txt
file HTSeq/StepVector.py (for module HTSeq.StepVector) not found
reading manifest file 'HTSeq.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
no previously-included directories found matching 'example_data'
no previously-included directories found matching 'test'
warning: no previously-included files found matching 'todo.txt'
writing manifest file 'HTSeq.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-10.4-x86_64/egg
running install_lib
running build_py
file HTSeq/StepVector.py (for module HTSeq.StepVector) not found
creating build
creating build/lib.macosx-10.4-x86_64-2.7
creating build/lib.macosx-10.4-x86_64-2.7/HTSeq
copying HTSeq/__init__.py -> build/lib.macosx-10.4-x86_64-2.7/HTSeq
copying HTSeq/_HTSeq_internal.py -> build/lib.macosx-10.4-x86_64-2.7/HTSeq
copying HTSeq/_version.py -> build/lib.macosx-10.4-x86_64-2.7/HTSeq
creating build/lib.macosx-10.4-x86_64-2.7/HTSeq/scripts
copying HTSeq/scripts/__init__.py -> build/lib.macosx-10.4-x86_64-2.7/HTSeq/scripts
copying HTSeq/scripts/qa.py -> build/lib.macosx-10.4-x86_64-2.7/HTSeq/scripts
copying HTSeq/scripts/count.py -> build/lib.macosx-10.4-x86_64-2.7/HTSeq/scripts
file HTSeq/StepVector.py (for module HTSeq.StepVector) not found
running build_ext
building 'HTSeq._HTSeq' extension
creating build/temp.macosx-10.4-x86_64-2.7
creating build/temp.macosx-10.4-x86_64-2.7/src
gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/lib/python2.7/site-packages/numpy-1.7.0.dev_3cb783e_20120427-py2.7-macosx-10.7-x86_64.egg/numpy/core/include -I/usr/local/include/python2.7 -c src/_HTSeq.c -o build/temp.macosx-10.4-x86_64-2.7/src/_HTSeq.o -w
gcc: error: src/_HTSeq.c: No such file or directory
gcc: fatal error: no input files
compilation terminated.
error: command 'gcc' failed with exit status 1

Simon Anders · 05-02-2012, 03:54 AM

Please start over and follow the instructions. Especially, note that the instructions do not ask you to run 'clean' or 'build_it'.

garima · 03-29-2013, 12:06 AM

Hi,

I am trying to install HTseq on our cluster(not root user) but it is giving me error while building.

PHP Code:


			
Could not import 'setuptools', falling back to 'distutils'.

running build

running build_py

creating build

creating build/lib.linux-x86_64-2.6

creating build/lib.linux-x86_64-2.6/HTSeq

copying HTSeq/__init__.py -> build/lib.linux-x86_64-2.6/HTSeq

copying HTSeq/_HTSeq_internal.py -> build/lib.linux-x86_64-2.6/HTSeq

copying HTSeq/StepVector.py -> build/lib.linux-x86_64-2.6/HTSeq

copying HTSeq/_version.py -> build/lib.linux-x86_64-2.6/HTSeq

creating build/lib.linux-x86_64-2.6/HTSeq/scripts

copying HTSeq/scripts/__init__.py -> build/lib.linux-x86_64-2.6/HTSeq/scripts

copying HTSeq/scripts/qa.py -> build/lib.linux-x86_64-2.6/HTSeq/scripts

copying HTSeq/scripts/count.py -> build/lib.linux-x86_64-2.6/HTSeq/scripts

running build_ext

building 'HTSeq._HTSeq' extension

creating build/temp.linux-x86_64-2.6

creating build/temp.linux-x86_64-2.6/src

icc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC -I/data/gkushwah/xulab/garima/tools/numpy-1.7.1rc1/lib/python2.6/site-packages/numpy/core/include -I/share/sw/python/current/include/python2.6 -c src/_HTSeq.c -o build/temp.linux-x86_64-2.6/src/_HTSeq.o -w

icc -pthread -shared build/temp.linux-x86_64-2.6/src/_HTSeq.o -o build/lib.linux-x86_64-2.6/HTSeq/_HTSeq.so

building 'HTSeq._StepVector' extension

icc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC -I/share/sw/python/current/include/python2.6 -c src/StepVector_wrap.cxx -o build/temp.linux-x86_64-2.6/src/StepVector_wrap.o -w

icpc -pthread -shared build/temp.linux-x86_64-2.6/src/StepVector_wrap.o src/step_vector.h -o build/lib.linux-x86_64-2.6/HTSeq/_StepVector.so

ld: /tmp/icpc4Ax1zp.o: relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC

/tmp/icpc4Ax1zp.o: could not read symbols: Bad value

error: command 'icpc' failed with exit status 1

Any suggestion?

Simon Anders · 04-03-2013, 06:37 AM

First of all: Please give complete information, when asking a question. It is not nice that I have to guess that your are using Linux and forgot to mention this although you can see that this thread is all about Mac OS. Which Linux distribution? Which Python? Is this your desktop PC or some centrally administered server?

Your Python is using Intel's C compiler (icc) instead of the GNU C compiler (gcc), which is used by virtually all Linux distribution. This hence does not seem to be a standard Python installation. You will have to try again with a more standard setup or ask the person for help who had the qeustionable idea of deploying an icc-built Python.

alexGrenoble · 11-12-2015, 08:08 AM

Hi,

I want to install htseq-count on a server (unix).
Here http://www-huber.embl.de/users/ander...l.html#install
they have for linux,mac and windows but not unix.

Let me know if you have any idea.

GenoMax · 11-12-2015, 08:22 AM

Quote:

Originally Posted by alexGrenoble

Hi,

I want to install htseq-count on a server (unix).
Here http://www-huber.embl.de/users/ander...l.html#install
they have for linux,mac and windows but not unix.

Let me know if you have any idea.

linux is a unix-like OS. So use the linux version.

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04-30-2012, 10:11 PM	#4
yifangt Member Location: Canada Join Date: Feb 2011 Posts: 61	HTSeq error with Ubuntu 11.10 Hi Simon! I met similar problem when I tried to install HTSeq-0.5.3p3. Read the other posts on similar problem in this forum and google, not direct clear solution yet. Code: Could not import 'setuptools', falling back to 'distutils'. But the rest went fine. Modified the .bashrc file as suggested by ngsseq (which seems for Mac OS, but gave it shot just in case!) still did not work. My python version is 2.7.2+ Any news for this Bug? Thanks! Last edited by yifangt; 04-30-2012 at 10:20 PM. Reason: small errors

04-30-2012, 11:43 PM	#5
yifangt Member Location: Canada Join Date: Feb 2011 Posts: 61	HTSeq error with Ubuntu 11.10: [SOLVED] Just in case anyone met the same problem. First updated my python to python3.2, still not working. Should have paid attention on the instruction (>=2.5 PYTHON <3.0). After a couple of try found out my problem is related to setuptools and python 3.2. 1) I had setuptools3 instead of setuptools. Decided to have both. After this, building from the source code went well, but met problem with Code: python setup.py install on line 12 of setup.py. Thought of the python version. 2) symbolic link my python to /usr/bin/python2.7.2 instead of /usr/bin/python3.2. Worked! And when I came back also found new version was released in another post, which does not need setuptools. Good luck!

03-29-2013, 12:06 AM	#10
garima Junior Member Location: Missouri Join Date: Jul 2012 Posts: 1	HTseq build error Hi, I am trying to install HTseq on our cluster(not root user) but it is giving me error while building. PHP Code: Could not import 'setuptools', falling back to 'distutils'. running build running build_py creating build creating build/lib.linux-x86_64-2.6 creating build/lib.linux-x86_64-2.6/HTSeq copying HTSeq/__init__.py -> build/lib.linux-x86_64-2.6/HTSeq copying HTSeq/_HTSeq_internal.py -> build/lib.linux-x86_64-2.6/HTSeq copying HTSeq/StepVector.py -> build/lib.linux-x86_64-2.6/HTSeq copying HTSeq/_version.py -> build/lib.linux-x86_64-2.6/HTSeq creating build/lib.linux-x86_64-2.6/HTSeq/scripts copying HTSeq/scripts/__init__.py -> build/lib.linux-x86_64-2.6/HTSeq/scripts copying HTSeq/scripts/qa.py -> build/lib.linux-x86_64-2.6/HTSeq/scripts copying HTSeq/scripts/count.py -> build/lib.linux-x86_64-2.6/HTSeq/scripts running build_ext building 'HTSeq._HTSeq' extension creating build/temp.linux-x86_64-2.6 creating build/temp.linux-x86_64-2.6/src icc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC -I/data/gkushwah/xulab/garima/tools/numpy-1.7.1rc1/lib/python2.6/site-packages/numpy/core/include -I/share/sw/python/current/include/python2.6 -c src/_HTSeq.c -o build/temp.linux-x86_64-2.6/src/_HTSeq.o -w icc -pthread -shared build/temp.linux-x86_64-2.6/src/_HTSeq.o -o build/lib.linux-x86_64-2.6/HTSeq/_HTSeq.so building 'HTSeq._StepVector' extension icc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC -I/share/sw/python/current/include/python2.6 -c src/StepVector_wrap.cxx -o build/temp.linux-x86_64-2.6/src/StepVector_wrap.o -w icpc -pthread -shared build/temp.linux-x86_64-2.6/src/StepVector_wrap.o src/step_vector.h -o build/lib.linux-x86_64-2.6/HTSeq/_StepVector.so ld: /tmp/icpc4Ax1zp.o: relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /tmp/icpc4Ax1zp.o: could not read symbols: Bad value error: command 'icpc' failed with exit status 1 Any suggestion?

04-06-2012, 03:15 PM	#2
Simon Anders Senior Member Location: Heidelberg, Germany Join Date: Feb 2010 Posts: 994	You are not supposed to run './build_it'. Rather, install HTSeq as you would install any other Python package, by running 'python setup.py install'. And read the installation instructions, please.

04-07-2012, 12:53 AM	#3
ngsseq Junior Member Location: earth Join Date: Jul 2011 Posts: 5	Hi sarosh, I installed HTSeq on Lion a few days ago. I got the same error message. I searched around and found a solution below: on the command line, add “export CC=gcc" into ~/.bash_profile, then “source ~/.bash_profile". I wish it would help. Regards, ngsseq

05-01-2012, 12:42 AM	#6
Simon Anders Senior Member Location: Heidelberg, Germany Join Date: Feb 2010 Posts: 994	You don't need setuptools, distutils works just fine. (This is what a "fallback" means.)

05-02-2012, 03:54 AM	#9
Simon Anders Senior Member Location: Heidelberg, Germany Join Date: Feb 2010 Posts: 994	Please start over and follow the instructions. Especially, note that the instructions do not ask you to run 'clean' or 'build_it'.

04-03-2013, 06:37 AM	#11
Simon Anders Senior Member Location: Heidelberg, Germany Join Date: Feb 2010 Posts: 994	First of all: Please give complete information, when asking a question. It is not nice that I have to guess that your are using Linux and forgot to mention this although you can see that this thread is all about Mac OS. Which Linux distribution? Which Python? Is this your desktop PC or some centrally administered server? Your Python is using Intel's C compiler (icc) instead of the GNU C compiler (gcc), which is used by virtually all Linux distribution. This hence does not seem to be a standard Python installation. You will have to try again with a more standard setup or ask the person for help who had the qeustionable idea of deploying an icc-built Python.

11-12-2015, 08:08 AM	#12
alexGrenoble Junior Member Location: grenoble Join Date: Nov 2013 Posts: 2	Hi, I want to install htseq-count on a server (unix). Here http://www-huber.embl.de/users/ander...l.html#install they have for linux,mac and windows but not unix. Let me know if you have any idea.