Installation failure

[Susanne Schindler]

Hi all,

I tried to install gc3pie on my laptop with ubuntu, but the installation
failed due to

[...]

Command "/home/sschindl/gc3pie/bin/python -u -c "import setuptools, tokenize;__f
ile__='/tmp/pip-build-iBZLJ1/cffi/setup.py';exec(compile(getattr(tokenize, 'open
', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --r
ecord /tmp/pip-tL8gZh-record/install-record.txt --single-version-externally-mana
ged --compile --install-headers /home/sschindl/gc3pie/include/site/python2.7/cff
i" failed with error code 1 in /tmp/pip-build-iBZLJ1/cffi/
Traceback (most recent call last):
File "install.py", line 983, in <module>
main()
File "install.py", line 137, in main
install_gc3pie_from_pypi(options.target, options.features)
File "install.py", line 720, in install_gc3pie_from_pypi
.format(features_for_pip=str.join(' ', features), **locals()))
File "install.py", line 957, in run_in_virtualenv
check_call(cmd, shell=True)
File "/usr/lib/python2.7/subprocess.py", line 511, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '.
/home/sschindl/gc3pie/bin/activate; pip install 'gc3pie'' returned non-zero
exit status 1

The complete output is below. I would be most grateful if you could
provide me with any tips. Many thanks,
Susanne

----------------------------------------------------------
sschindl@zoo-sschindllt:~$ python install.py

==========================
GC3Pie installation script
==========================

This script installs *latest stable version* of GC3Pie in '/home/sschindl/gc3pie
'.

If you encounter any problem running this script, please contact
the GC3Pie team by sending an email to gc3...@googlegroups.com.

Remember to attach the full output of the script, in order to help us
to identify the problem.

Installation info:

Destination directory: /home/sschindl/gc3pie
Overwrite existing dir: ask
Python executable: /usr/bin/python
Ask for confirmation: yes
Install unreleased code: no
Install gc3apps: yes
Optional features: NONE
Installer script version: 2.0.0


Are you ready to continue? [Y/n] Y

Destination directory '/home/sschindl/gc3pie' already exists.
I can wipe it out in order to make a new installation,
but this means any files in that directory, and the ones
underneath it will be deleted.


Do you want to wipe the installation directory '/home/sschindl/gc3pie' ? [Y/n]
<GC3Pie install> INFO: Deleting directory '/home/sschindl/gc3pie' as request
ed ...
Already using interpreter /usr/bin/python
New python executable in /home/sschindl/gc3pie/bin/python
Installing setuptools..............................done.
Installing pip...............................done.
<GC3Pie install> INFO: Created Python virtual environment in '/home/sschindl
/gc3pie'
<GC3Pie install> INFO: Trying to install or upgrade setuptools ...
<GC3Pie install> INFO: `easy_install` is available, using it to upgrade setu
ptools
Searching for setuptools
Reading http://pypi.python.org/simple/setuptools/
Best match: setuptools 22.0.5
Processing setuptools-22.0.5-py2.7.egg
Removing setuptools 0.6c11 from easy-install.pth file
Adding setuptools 22.0.5 to easy-install.pth file
Installing easy_install script to /home/sschindl/gc3pie/bin
Installing easy_install-2.7 script to /home/sschindl/gc3pie/bin

Using /home/sschindl/gc3pie/lib/python2.7/site-packages/setuptools-22.0.5-py2.7.
egg
Processing dependencies for setuptools
Finished processing dependencies for setuptools
<GC3Pie install> INFO: Installing GC3Pie released code from PyPI ...
<GC3Pie install> INFO: Installing GC3Pie from PyPI package with '/home/sschi
ndl/gc3pie/bin/pip' ...
Collecting gc3pie
Using cached gc3pie-2.4.2.tar.gz
Collecting paramiko (from gc3pie)
Using cached paramiko-2.0.0-py2.py3-none-any.whl
Requirement already satisfied (use --upgrade to upgrade): pycrypto in /usr/lib/p
ython2.7/dist-packages (from gc3pie)
Collecting prettytable (from gc3pie)
Using cached prettytable-0.7.2.zip
Collecting pyCLI (from gc3pie)
Using cached pyCLI-2.0.3.tar.gz
Collecting sqlalchemy (from gc3pie)
Using cached SQLAlchemy-1.0.13.tar.gz
Collecting parsedatetime (from gc3pie)
Using cached parsedatetime-2.1-py2-none-any.whl
Collecting pyasn1>=0.1.7 (from paramiko->gc3pie)
Using cached pyasn1-0.1.9-py2.py3-none-any.whl
Collecting cryptography>=1.1 (from paramiko->gc3pie)
Using cached cryptography-1.4.tar.gz
Collecting idna>=2.0 (from cryptography>=1.1->paramiko->gc3pie)
Using cached idna-2.1-py2.py3-none-any.whl
Collecting six>=1.4.1 (from cryptography>=1.1->paramiko->gc3pie)
Using cached six-1.10.0-py2.py3-none-any.whl
Requirement already satisfied (use --upgrade to upgrade): setuptools>=11.3 in ./
gc3pie/lib/python2.7/site-packages/setuptools-22.0.5-py2.7.egg (from cryptograph
y>=1.1->paramiko->gc3pie)
Collecting enum34 (from cryptography>=1.1->paramiko->gc3pie)
Using cached enum34-1.1.6-py2-none-any.whl
Collecting ipaddress (from cryptography>=1.1->paramiko->gc3pie)
Using cached ipaddress-1.0.16-py27-none-any.whl
Collecting cffi>=1.4.1 (from cryptography>=1.1->paramiko->gc3pie)
Using cached cffi-1.6.0.tar.gz
Collecting pycparser (from cffi>=1.4.1->cryptography>=1.1->paramiko->gc3pie)
Using cached pycparser-2.14.tar.gz
Installing collected packages: pyasn1, idna, six, enum34, ipaddress, pycparser,
cffi, cryptography, paramiko, prettytable, pyCLI, sqlalchemy, parsedatetime, gc3
pie
Running setup.py install for pycparser ... done
Running setup.py install for cffi ... error
Complete output from command /home/sschindl/gc3pie/bin/python -u -c "import
setuptools, tokenize;__file__='/tmp/pip-build-iBZLJ1/cffi/setup.py';exec(compile
(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file_
_, 'exec'))" install --record /tmp/pip-tL8gZh-record/install-record.txt --single
-version-externally-managed --compile --install-headers /home/sschindl/gc3pie/in
clude/site/python2.7/cffi:
Package libffi was not found in the pkg-config search path.
Perhaps you should add the directory containing `libffi.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libffi' found
Package libffi was not found in the pkg-config search path.
Perhaps you should add the directory containing `libffi.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libffi' found
Package libffi was not found in the pkg-config search path.
Perhaps you should add the directory containing `libffi.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libffi' found
Package libffi was not found in the pkg-config search path.
Perhaps you should add the directory containing `libffi.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libffi' found
Package libffi was not found in the pkg-config search path.
Perhaps you should add the directory containing `libffi.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libffi' found
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/cffi
copying cffi/api.py -> build/lib.linux-x86_64-2.7/cffi
copying cffi/gc_weakref.py -> build/lib.linux-x86_64-2.7/cffi
copying cffi/cffi_opcode.py -> build/lib.linux-x86_64-2.7/cffi
copying cffi/commontypes.py -> build/lib.linux-x86_64-2.7/cffi
copying cffi/model.py -> build/lib.linux-x86_64-2.7/cffi
copying cffi/__init__.py -> build/lib.linux-x86_64-2.7/cffi
copying cffi/lock.py -> build/lib.linux-x86_64-2.7/cffi
copying cffi/backend_ctypes.py -> build/lib.linux-x86_64-2.7/cffi
copying cffi/vengine_cpy.py -> build/lib.linux-x86_64-2.7/cffi
copying cffi/setuptools_ext.py -> build/lib.linux-x86_64-2.7/cffi
copying cffi/recompiler.py -> build/lib.linux-x86_64-2.7/cffi
copying cffi/cparser.py -> build/lib.linux-x86_64-2.7/cffi
copying cffi/vengine_gen.py -> build/lib.linux-x86_64-2.7/cffi
copying cffi/ffiplatform.py -> build/lib.linux-x86_64-2.7/cffi
copying cffi/verifier.py -> build/lib.linux-x86_64-2.7/cffi
copying cffi/_cffi_include.h -> build/lib.linux-x86_64-2.7/cffi
copying cffi/parse_c_type.h -> build/lib.linux-x86_64-2.7/cffi
copying cffi/_embedding.h -> build/lib.linux-x86_64-2.7/cffi
running build_ext
building '_cffi_backend' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/c
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-pro
totypes -fPIC -DUSE__THREAD -I/usr/include/ffi -I/usr/include/libffi -I/usr/incl
ude/python2.7 -c c/_cffi_backend.c -o build/temp.linux-x86_64-2.7/c/_cffi_backen
d.o
c/_cffi_backend.c:15:17: fatal error: ffi.h: No such file or directory
compilation terminated.
error: command 'gcc' failed with exit status 1

----------------------------------------
Command "/home/sschindl/gc3pie/bin/python -u -c "import setuptools, tokenize;__f
ile__='/tmp/pip-build-iBZLJ1/cffi/setup.py';exec(compile(getattr(tokenize, 'open
', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --r
ecord /tmp/pip-tL8gZh-record/install-record.txt --single-version-externally-mana
ged --compile --install-headers /home/sschindl/gc3pie/include/site/python2.7/cff
i" failed with error code 1 in /tmp/pip-build-iBZLJ1/cffi/
Traceback (most recent call last):
File "install.py", line 983, in <module>
main()
File "install.py", line 137, in main
install_gc3pie_from_pypi(options.target, options.features)
File "install.py", line 720, in install_gc3pie_from_pypi
.format(features_for_pip=str.join(' ', features), **locals()))
File "install.py", line 957, in run_in_virtualenv
check_call(cmd, shell=True)
File "/usr/lib/python2.7/subprocess.py", line 511, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '.
/home/sschindl/gc3pie/bin/activate; pip install 'gc3pie'' returned non-zero
exit status 1

[Riccardo Murri]

Hi Susanne,


(Susanne Schindler, Tue, Jun 07, 2016 at 02:32:17PM +0000:)

> I tried to install gc3pie on my laptop with ubuntu, but the installation
> failed due to
>
> [...]

> building '_cffi_backend' extension
> [...]

> gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-pro
> totypes -fPIC -DUSE__THREAD -I/usr/include/ffi -I/usr/include/libffi -I/usr/incl
> ude/python2.7 -c c/_cffi_backend.c -o build/temp.linux-x86_64-2.7/c/_cffi_backen
> d.o
> c/_cffi_backend.c:15:17: fatal error: ffi.h: No such file or directory

Can you please try this command, and then re-run the GC3Pie installation
script?

sudo apt-get install libffi-dev

I have just uploaded version 2.0.1 of the install script, which should
catch this error and give appropriate instructions.

Ciao,
R

--
Riccardo Murri, Anna-Heer-Strasse 10, CH-8057 Zürich, Switzerland

[Susanne Schindler]

Ciao Riccardo,

Riccardo Murri <riccardo.murri@...> writes:

>
> Can you please try this command, and then re-run the GC3Pie installation
> script?
>
> sudo apt-get install libffi-dev
>
> I have just uploaded version 2.0.1 of the install script, which should
> catch this error and give appropriate instructions.
>
> Ciao,
> R

Thank you very much, this worked and the installation has successfully finished.
However, the virtual environment cannot be enabled yet:

sschindl@zoo-sschindllt:~$ /home/sschindl/gc3pie/bin/activate
bash: /home/sschindl/gc3pie/bin/activate: Permission denied
sschindl@zoo-sschindllt:~/gc3pie/bin$ chmod 700 activate
sschindl@zoo-sschindllt:~/gc3pie/bin$ ./activate
sschindl@zoo-sschindllt:~/gc3pie/bin$ source ~/gc3pie/bin/sc-authenticate.sh
bash: /home/sschindl/gc3pie/bin/sc-authenticate.sh: No such file or directory

also gc3utils isn't found:
sschindl@zoo-sschindllt:~/gc3pie/bin$ gc3utils --help
gc3utils: command not found

The output from the installation is copied below. Thank you very much for
your help!
Susanne

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

Do you want to wipe the installation directory '/home/sschindl/gc3pie' ? [Y/n]
<GC3Pie install> INFO: Deleting directory '/home/sschindl/gc3pie' as

requested ...

Already using interpreter /usr/bin/python
New python executable in /home/sschindl/gc3pie/bin/python
Installing setuptools..............................done.
Installing pip...............................done.
<GC3Pie install> INFO: Created Python virtual environment in
'/home/sschindl/gc3pie'
<GC3Pie install> INFO: Trying to install or upgrade setuptools ...
<GC3Pie install> INFO: `easy_install` is available, using it to upgrade
setuptools
Searching for setuptools
Reading http://pypi.python.org/simple/setuptools/

Best match: setuptools 23.0.0
Processing setuptools-23.0.0-py2.7.egg

Removing setuptools 0.6c11 from easy-install.pth file

Adding setuptools 23.0.0 to easy-install.pth file

Installing easy_install script to /home/sschindl/gc3pie/bin
Installing easy_install-2.7 script to /home/sschindl/gc3pie/bin

Using

/home/sschindl/gc3pie/lib/python2.7/site-packages/setuptools-23.0.0-py2.7.egg

Processing dependencies for setuptools
Finished processing dependencies for setuptools
<GC3Pie install> INFO: Installing GC3Pie released code from PyPI ...
<GC3Pie install> INFO: Installing GC3Pie from PyPI package with
'/home/sschindl/gc3pie/bin/pip' ...
Collecting gc3pie

/home/sschindl/gc3pie/local/lib/python2.7/site-packages/pip-8.1.2-py2.7.egg/pip/
_vendor/requests/packages/urllib3/util/ssl_.py:318:
SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name
Indication) extension to TLS is not available on this platform. This may
cause the server to present an incorrect TLS certificate, which can cause
validation failures. You can upgrade to a newer version of Python to solve
this. For more information, see
https://urllib3.readthedocs.org/en/latest/security.html#snimissingwarning.
SNIMissingWarning
/home/sschindl/gc3pie/local/lib/python2.7/site-packages/pip-8.1.2-py2.7.egg/pip/
_vendor/requests/packages/urllib3/util/ssl_.py:122:
InsecurePlatformWarning: A true SSLContext object is not available. This
prevents urllib3 from configuring SSL appropriately and may cause certain
SSL connections to fail. You can upgrade to a newer version of Python to
solve this. For more information, see
https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning.
InsecurePlatformWarning

Using cached gc3pie-2.4.2.tar.gz
Collecting paramiko (from gc3pie)
Using cached paramiko-2.0.0-py2.py3-none-any.whl
Requirement already satisfied (use --upgrade to upgrade): pycrypto in

/usr/lib/python2.7/dist-packages (from gc3pie)

Collecting prettytable (from gc3pie)
Using cached prettytable-0.7.2.zip
Collecting pyCLI (from gc3pie)
Using cached pyCLI-2.0.3.tar.gz
Collecting sqlalchemy (from gc3pie)
Using cached SQLAlchemy-1.0.13.tar.gz
Collecting parsedatetime (from gc3pie)
Using cached parsedatetime-2.1-py2-none-any.whl
Collecting pyasn1>=0.1.7 (from paramiko->gc3pie)
Using cached pyasn1-0.1.9-py2.py3-none-any.whl
Collecting cryptography>=1.1 (from paramiko->gc3pie)
Using cached cryptography-1.4.tar.gz
Collecting idna>=2.0 (from cryptography>=1.1->paramiko->gc3pie)
Using cached idna-2.1-py2.py3-none-any.whl
Collecting six>=1.4.1 (from cryptography>=1.1->paramiko->gc3pie)
Using cached six-1.10.0-py2.py3-none-any.whl
Requirement already satisfied (use --upgrade to upgrade): setuptools>=11.3

in ./gc3pie/lib/python2.7/site-packages/setuptools-23.0.0-py2.7.egg (from
cryptography>=1.1->paramiko->gc3pie)

Collecting enum34 (from cryptography>=1.1->paramiko->gc3pie)
Using cached enum34-1.1.6-py2-none-any.whl
Collecting ipaddress (from cryptography>=1.1->paramiko->gc3pie)
Using cached ipaddress-1.0.16-py27-none-any.whl
Collecting cffi>=1.4.1 (from cryptography>=1.1->paramiko->gc3pie)
Using cached cffi-1.6.0.tar.gz
Collecting pycparser (from cffi>=1.4.1->cryptography>=1.1->paramiko->gc3pie)
Using cached pycparser-2.14.tar.gz
Installing collected packages: pyasn1, idna, six, enum34, ipaddress,
pycparser, cffi, cryptography, paramiko, prettytable, pyCLI, sqlalchemy,
parsedatetime, gc3pie
Running setup.py install for pycparser ... done

Running setup.py install for cffi ... done
Running setup.py install for cryptography ... done
Running setup.py install for prettytable ... done
Running setup.py install for pyCLI ... done
Running setup.py install for sqlalchemy ... done
Running setup.py install for gc3pie ... done
Successfully installed cffi-1.6.0 cryptography-1.4 enum34-1.1.6 gc3pie-2.4.2
idna-2.1 ipaddress-1.0.16 paramiko-2.0.0 parsedatetime-2.1 prettytable-0.7.2
pyCLI-2.0.3 pyasn1-0.1.9 pycparser-2.14 six-1.10.0 sqlalchemy-1.0.13
/home/sschindl/gc3pie/local/lib/python2.7/site-packages/pip-8.1.2-py2.7.egg/pip/
_vendor/requests/packages/urllib3/util/ssl_.py:122:
InsecurePlatformWarning: A true SSLContext object is not available. This
prevents urllib3 from configuring SSL appropriately and may cause certain
SSL connections to fail. You can upgrade to a newer version of Python to
solve this. For more information, see
https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning.
InsecurePlatformWarning
<GC3Pie install> INFO: Installing extra applications into
'/home/sschindl/gc3pie/bin' ...
<GC3Pie install> INFO: /home/sschindl/gc3pie/gc3apps/ggamess.py ->
/home/sschindl/gc3pie/bin/ggamess.py
<GC3Pie install> INFO: /home/sschindl/gc3pie/gc3apps/gridrun.py ->
/home/sschindl/gc3pie/bin/gridrun.py
<GC3Pie install> INFO: /home/sschindl/gc3pie/gc3apps/gcodeml.py ->
/home/sschindl/gc3pie/bin/gcodeml.py
<GC3Pie install> INFO: /home/sschindl/gc3pie/gc3apps/grundb.py ->
/home/sschindl/gc3pie/bin/grundb.py

===============================
Installation of GC3Pie is done!
===============================

In order to work with GC3Pie you have to enable the virtual
environment with the command:

. /home/sschindl/gc3pie/bin/activate

You need to run the above command on every new shell you open before
using GC3Pie commands, but just once per session.

If the shell's prompt starts with '(gc3pie)' it means that the virtual
environment has been enabled.

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

[Riccardo Murri]

Hello Susanne:

On 10 June 2016 at 21:37, Susanne Schindler

<susanne....@ieu.uzh.ch> wrote:
> sschindl@zoo-sschindllt:~$ /home/sschindl/gc3pie/bin/activate
> bash: /home/sschindl/gc3pie/bin/activate: Permission denied

Note, the correct command to issue is:

. /home/sschindl/gc3pie/bin/activate

that is, dot+space+/home/...

If you omit the dot+space part at the beginning, it won't work.

Ciao,
R

[Susanne Schindler]

Hi Riccardo,

> > sschindl <at> zoo-sschindllt:~$ /home/sschindl/gc3pie/bin/activate

> > bash: /home/sschindl/gc3pie/bin/activate: Permission denied
>
> Note, the correct command to issue is:
>
> . /home/sschindl/gc3pie/bin/activate
>
> that is, dot+space+/home/...
>
> If you omit the dot+space part at the beginning, it won't work.

Yes, I did overlook that. Sorry and many thanks indeed!
Cheers, Susanne