Installation v1.9.2.0 on Ubuntu 14.04.05 failed systematically

[imbeaud]

Hi,

We try to install oncotator latest release (v1.9.2.0) on a Ubuntu 14.04.5 LTS. But systematically failed

First python setup.py install failed due to some reason
So we have installed all dependancies manually as described in http://gatkforums.broadinstitute.org/gatk/discussion/4153/what-are-the-platform-requirements-and-software-dependencies-for-running-oncotator
Then retrying installation resulted in a error with the following message:
error: Setup script exited with error: Command "x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -I/usr/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/private -Ibuild/src.linux-x86_64-2.7/numpy/core/src/private -Ibuild/src.linux-x86_64-2.7/numpy/core/src/private -c build/src.linux-x86_64-2.7/numpy/core/src/npymath/ieee754.c -o build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy/core/src/npymath/ieee754.o" failed with exit status 1

Is there any solution or obvious manner to successfull our installation.
Many thanks for your help

/ Sandrine Imbeaud

[LeeTL1220]

Did you create a virtual environment with the create_virtual_env script? The forum should have instructions - sorry I don't have the link handy right now. On Feb 10, 2017 04:32, "imbeaud" <notifications@github.com> wrote: Hi, We try to install oncotator latest release (v1.9.2.0) on a Ubuntu 14.04.5 LTS. But systematically failed First python setup.py install failed due to some reason So we have installed all dependancies manually as described in http://gatkforums.broadinstitute.org/gatk/discussion/4153/what-are-the- platform-requirements-and-software-dependencies-for-running-oncotator Then retrying installation resulted in a error with the following message: error: Setup script exited with error: Command "x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -I/usr/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/private -Ibuild/src.linux-x86_64-2.7/numpy/core/src/private -Ibuild/src.linux-x86_64-2.7/numpy/core/src/private -c build/src.linux-x86_64-2.7/numpy/core/src/npymath/ieee754.c -o build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/ numpy/core/src/npymath/ieee754.o" failed with exit status 1 Is there any solution or obvious manner to successfull our installation. Many thanks for your help / Sandrine Imbeaud — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#358>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACDXkwELoGcKqZeTxEvKfAjtYiEdpnLZks5rbC6cgaJpZM4L9LA0> .

[imbeaud]

Hi Lee, Not I did not. Is it mandatory, even if all required libraries were installed? Kind Regards / Sandrine Le 2/10/2017 à 11:37 AM, Lee Lichtenstein a écrit :

…

Did you create a virtual environment with the create_virtual_env script? The forum should have instructions - sorry I don't have the link handy right now. On Feb 10, 2017 04:32, "imbeaud" ***@***.***> wrote: Hi, We try to install oncotator latest release (v1.9.2.0) on a Ubuntu 14.04.5 LTS. But systematically failed First python setup.py install failed due to some reason So we have installed all dependancies manually as described in http://gatkforums.broadinstitute.org/gatk/discussion/4153/what-are-the- platform-requirements-and-software-dependencies-for-running-oncotator Then retrying installation resulted in a error with the following message: error: Setup script exited with error: Command "x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -I/usr/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/private -Ibuild/src.linux-x86_64-2.7/numpy/core/src/private -Ibuild/src.linux-x86_64-2.7/numpy/core/src/private -c build/src.linux-x86_64-2.7/numpy/core/src/npymath/ieee754.c -o build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/ numpy/core/src/npymath/ieee754.o" failed with exit status 1 Is there any solution or obvious manner to successfull our installation. Many thanks for your help / Sandrine Imbeaud — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#358>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACDXkwELoGcKqZeTxEvKfAjtYiEdpnLZks5rbC6cgaJpZM4L9LA0> . — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#358 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AKH1TfQYpuJzYE_G5-U9QEpXT6-QrKq1ks5rbD3ggaJpZM4L9LA0>.

-- Sandrine Imbeaud INSERM, UMR U-1162 Université Paris Descartes - Paris Diderot - Paris 13 Unité Génomique Fonctionnelle des Tumeurs Solides 27 rue Juliette Dodu F75010 Paris, France TEL: +33 (0)1 53 72 51 98 FAX: +33 (0)1 53 72 51 92 MOBILE: +33 (0)6 12 69 80 29 http://www.inserm-u674.net/

[LeeTL1220]

Technically no, but it is much easier....You are getting an error during the install of numpy. This is independent of Oncotator. On Feb 10, 2017 05:56, "imbeaud" <notifications@github.com> wrote: Hi Lee, Not I did not. Is it mandatory, even if all required libraries were installed? Kind Regards / Sandrine Le 2/10/2017 à 11:37 AM, Lee Lichtenstein a écrit :

Did you create a virtual environment with the create_virtual_env script? The forum should have instructions - sorry I don't have the link handy right now. On Feb 10, 2017 04:32, "imbeaud" ***@***.***> wrote: Hi, We try to install oncotator latest release (v1.9.2.0) on a Ubuntu 14.04.5 LTS. But systematically failed First python setup.py install failed due to some reason So we have installed all dependancies manually as described in http://gatkforums.broadinstitute.org/gatk/discussion/4153/what-are-the- platform-requirements-and-software-dependencies-for-running-oncotator Then retrying installation resulted in a error with the following message: error: Setup script exited with error: Command "x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -I/usr/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/private -Ibuild/src.linux-x86_64-2.7/numpy/core/src/private -Ibuild/src.linux-x86_64-2.7/numpy/core/src/private -c build/src.linux-x86_64-2.7/numpy/core/src/npymath/ieee754.c -o build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/ numpy/core/src/npymath/ieee754.o" failed with exit status 1 Is there any solution or obvious manner to successfull our installation. Many thanks for your help / Sandrine Imbeaud — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#358>, or mute the thread <https://github.com/notifications/unsubscribe-auth/

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…

-- Sandrine Imbeaud INSERM, UMR U-1162 Université Paris Descartes - Paris Diderot - Paris 13 Unité Génomique Fonctionnelle des Tumeurs Solides 27 rue Juliette Dodu F75010 Paris, France TEL: +33 (0)1 53 72 51 98 <+33%201%2053%2072%2051%2098> FAX: +33 (0)1 53 72 51 92 <+33%201%2053%2072%2051%2092> MOBILE: +33 (0)6 12 69 80 29 <+33%206%2012%2069%2080%2029> http://www.inserm-u674.net/ — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#358 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACDXk7IqcnHxXOPwMyabwzYwJqkBvNLUks5rbEJBgaJpZM4L9LA0> .

[myszak18]

I faced the same issue even though I had numpy installed. In my case, removing numpy from install_requires in setup,py file helped.