Question: how to install python2.7-dev in Linux
0
gravatar for xiachongjing
2.7 years ago by
xiachongjing10
United States
xiachongjing10 wrote:

Dear all: I am trying to install Falcon for PacBio sequencing assembly. I got this error: command 'gcc' failed with exit status 1. I am using Python 2.7.10. It seems the solution is to install python2.7-dev. However, I do not have root privilege, so I cannot type "sudo apt-get update" "sudo apt-get install python2.7-dev"

Anybody can help me to install python2.7-dev? Or what else can I do to solve the error? Thanks in advance.

software error • 2.2k views
ADD COMMENTlink written 2.7 years ago by xiachongjing10

Pure systems questions are better suited for stackexchange.

How did you conclude that is what is the cause of the error you are getting?

ADD REPLYlink written 2.7 years ago by genomax65k

First, my Python is working since I successfully installed pypeFLOW following https://github.com/PacificBiosciences/FALCON/wiki/Setup%3A-Installation-and-Environment.

Second, I checked my gcc --version. I got " gcc (GCC) 4.8.2".

Then I search the error in google. Many people got this error, and fixed this error by installing python-dev.

Any ideas? Thanks

ADD REPLYlink written 2.7 years ago by xiachongjing10

If you managed to install pypeFLOW then the second step should work too. You should post all lines that may have error information in them.

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by genomax65k

Thanks. Here I post my command and the error information:

[cho.xia@login1 FALCON]$  /home/plant_pathology/cho.xia/software/Python-2.7.10/Python-2.7.10/python setup.py install --prefix=/home/plant_pathology/cho.xia/software/Python-2.7.10/Python-2.7.10

Installed /home/plant_pathology/cho.xia/fc_env/FALCON-integrate/FALCON/.eggs/networkx-1.10-py2.7.egg
/home/plant_pathology/cho.xia/software/Python-2.7.10/Python-2.7.10/lib/python2.7/site-packages/setuptools-25.1.6-py2.7.egg/setuptools/dist.py:364: UserWarning: Normalizing '0.7+git.d51ec37a4012eed6743a8b1118070771128e039a
' to '0.7+git.d51ec37a4012eed6743a8b1118070771128e039a'
running install
running bdist_egg
running egg_info
creating falcon_kit.egg-info
writing requirements to falcon_kit.egg-info/requires.txt
writing falcon_kit.egg-info/PKG-INFO
......
......
copying falcon_kit/util/system.py -> build/lib.linux-x86_64-2.7/falcon_kit/util
running build_ext
building 'ext_falcon' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/src
creating build/temp.linux-x86_64-2.7/src/c
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/plant_pathology/cho.xia/software/Python-2.7.10/Python-2.7.10/Include -I/home/plant_pathology/cho.xia/software/Python-2.7.10/Python-2.7.10 -c src/c/ext_falcon.c -o build/temp.linux-x86_64-2.7/src/c/ext_falcon.o -fPIC -O3 -fno-omit-frame-pointer
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/plant_pathology/cho.xia/software/Python-2.7.10/Python-2.7.10/Include -I/home/plant_pathology/cho.xia/software/Python-2.7.10/Python-2.7.10 -c src/c/DW_banded.c -o build/temp.linux-x86_64-2.7/src/c/DW_banded.o -fPIC -O3 -fno-omit-frame-pointer
/tmp/ccMJpWpP.s: Assembler messages:
/tmp/ccMJpWpP.s:151: Error: unknown .loc sub-directive `discriminator'
/tmp/ccMJpWpP.s:151: Error: junk at end of line, first unrecognized character is `2'
/tmp/ccMJpWpP.s:158: Error: unknown .loc sub-directive `discriminator'
/tmp/ccMJpWpP.s:158: Error: junk at end of line, first unrecognized character is `2'
......
/tmp/ccMJpWpP.s:937: Error: unknown .loc sub-directive `discriminator'
/tmp/ccMJpWpP.s:937: Error: junk at end of line, first unrecognized character is `2'
error: command 'gcc' failed with exit status 1

Please let me know if you need more information. Thanks so much for any help.

ADD REPLYlink modified 2.7 years ago by genomax65k • written 2.7 years ago by xiachongjing10

What OS are you using? Looks like it is 64-bit, correct?

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by genomax65k

[cho.xia@login1 ~]$ uname -a Linux login1 2.6.18-164.el5 #1 SMP Tue Aug 18 15:51:48 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux

Thanks.

ADD REPLYlink written 2.7 years ago by xiachongjing10

Based on some searching it is possible that you have an old version of binutils program (you seem to have a pretty old kernel so this is a possibility). Search for "binutils version" and see if you can determine the version of binutils you have. This would likely not be something you would be able to update so you would need to talk with your sys admins about options.

Does ld -v print version of binutils?

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by genomax65k

I don't why and what happened, I succeed in installing Falcon step. I just re-try my command: [cho.xia@login1 FALCON]$ /home/plant_pathology/cho.xia/software/Python-2.7.10/Python-2.7.10/python setup.py install --prefix=/home/plant_pathology/cho.xia/software/Python-2.7.10/Python-2.7.10

It's so wired. Thanks anyway.

ADD REPLYlink written 2.7 years ago by xiachongjing10

Long as it worked :-)

ADD REPLYlink written 2.7 years ago by genomax65k
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