app-deploy-qiime-1.5.0 installation errors
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Salim
May 10, 2012, 12:06:43 AM5/10/12
to qiime...@googlegroups.com
Hi,
I have been trying to install Qiime 1.5.0 using the deploy script but I keep on getting the following error for all the python dependent programs:
Output: /path/packages/qiime-1.5.0/python-2.7.1-release/bin/python: error while loading shared libraries: libpython2.7.so.1.0: cannot open shared object file: No such file or directory
DEPLOYMENT SUMMARY
Packages deployed successfully:
python
Packages skipped (assumed successful):
data-core, clearcut, raxml, data-lanemask, cdbtools, rtax, cytoscape, chimeraslayer, drisee, gg_otus, infernal, vienna, mothur, fasttree, pplacer, blast, parsinsert, r, muscle, rdpclassifier, cdhit, uclust
Packages failed to deploy:
ampliconnoise, numpy, pyzmq, SQLAlchemy, biom-format, pycogent, matplotlib, tornado, setuptools, pynast, pprospector, MySQL-python, qiime, sphinx, mpi4py, ipython
Many thanks in advance,
Salim
Antonio González Peña
May 10, 2012, 8:33:54 AM5/10/12
to qiime...@googlegroups.com
Hi Salim,
My guess is that you are not using Ubuntu 11 or 12, right? What kind
of OS are you using?
Anyway, the solution is that you modify the etc/qiime_1.5.0.conf file,
if this is the one that you are using and add at the end of the
python configuration this line: set-environment-variables-deploypath:
LD_LIBRARY_PATH=lib/. After making that modification your python
configuration should look like this:
[python]
version: 2.7.1
build-type: autoconf
release-file-name: Python-2.7.1.tgz
release-location:
ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/Python-2.7.1.tgz
relative-directory-add-to-path: bin
autoconf-configure-options: --enable-shared --with-zlib=/usr/include
--enable-unicode=ucs2 --enable-unicode=ucs4
set-environment-variables-deploypath: LD_LIBRARY_PATH=lib/
After that you have remove the previous python installation:
rm -r /path/packages/qiime-1.5.0/python-2.7.1-release/
and rerun the deploy.
Cheers.
--
Antonio González Peña
Research Assistant, Knight Lab
University of Colorado at Boulder
https://chem.colorado.edu/knightgroup/
My guess is that you are not using Ubuntu 11 or 12, right? What kind
of OS are you using?
Anyway, the solution is that you modify the etc/qiime_1.5.0.conf file,
if this is the one that you are using and add at the end of the
python configuration this line: set-environment-variables-deploypath:
LD_LIBRARY_PATH=lib/. After making that modification your python
configuration should look like this:
[python]
version: 2.7.1
build-type: autoconf
release-file-name: Python-2.7.1.tgz
release-location:
ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/Python-2.7.1.tgz
relative-directory-add-to-path: bin
autoconf-configure-options: --enable-shared --with-zlib=/usr/include
--enable-unicode=ucs2 --enable-unicode=ucs4
set-environment-variables-deploypath: LD_LIBRARY_PATH=lib/
After that you have remove the previous python installation:
rm -r /path/packages/qiime-1.5.0/python-2.7.1-release/
and rerun the deploy.
Cheers.
Antonio González Peña
Research Assistant, Knight Lab
University of Colorado at Boulder
https://chem.colorado.edu/knightgroup/
SeanB
May 10, 2012, 2:28:30 PM5/10/12
to Qiime Forum
Hi Antonio and Salim,
I had an identical problem while installing qiime 1.5.0 on our server
running ubuntu 10.04. I noticed that in the initial dependency
installation one install failed: libzmq-dev. I installed all the other
components and then ran the deploy script. The first time around I had
Salim's first set of errors, but with the python environment fix
almost everything installed except pyzmq failed to deploy.
To fix this I had to install a libzmq-dev, but it isn't available on
10.04. But I did find that you could use a backported version, libzmq-
dev (http://packages.ubuntu.com/natty-backports), so long as you first
install the backported versions of libpgm-5.1-0 and libzmq1. Once I
installed them in the order libpgm, libzmg1, and libzmq, I reran the
deployment as suggested, and the deployment completed all the packages
successfully.
Sean
On May 10, 8:33 am, Antonio González Peña <antgo...@gmail.com> wrote:
> Hi Salim,
>
> My guess is that you are not using Ubuntu 11 or 12, right? What kind
> of OS are you using?
>
> Anyway, the solution is that you modify the etc/qiime_1.5.0.conf file,
> if this is the one that you are using and add at the end of the
> python configuration this line: set-environment-variables-deploypath:
> LD_LIBRARY_PATH=lib/. After making that modification your python
> configuration should look like this:
> [python]
> version: 2.7.1
> build-type: autoconf
> release-file-name: Python-2.7.1.tgz
> release-location:ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/Python-2.7....
I had an identical problem while installing qiime 1.5.0 on our server
running ubuntu 10.04. I noticed that in the initial dependency
installation one install failed: libzmq-dev. I installed all the other
components and then ran the deploy script. The first time around I had
Salim's first set of errors, but with the python environment fix
almost everything installed except pyzmq failed to deploy.
To fix this I had to install a libzmq-dev, but it isn't available on
10.04. But I did find that you could use a backported version, libzmq-
dev (http://packages.ubuntu.com/natty-backports), so long as you first
install the backported versions of libpgm-5.1-0 and libzmq1. Once I
installed them in the order libpgm, libzmg1, and libzmq, I reran the
deployment as suggested, and the deployment completed all the packages
successfully.
Sean
On May 10, 8:33 am, Antonio González Peña <antgo...@gmail.com> wrote:
> Hi Salim,
>
> My guess is that you are not using Ubuntu 11 or 12, right? What kind
> of OS are you using?
>
> Anyway, the solution is that you modify the etc/qiime_1.5.0.conf file,
> if this is the one that you are using and add at the end of the
> python configuration this line: set-environment-variables-deploypath:
> LD_LIBRARY_PATH=lib/. After making that modification your python
> configuration should look like this:
> [python]
> version: 2.7.1
> build-type: autoconf
> release-file-name: Python-2.7.1.tgz
Antonio González Peña
May 10, 2012, 3:16:40 PM5/10/12
to qiime...@googlegroups.com
Glad it worked Sean. Thanks.
Please, check this thread:
http://groups.google.com/group/qiime-forum/browse_thread/thread/1f3e39e672faaacc
Please, check this thread:
http://groups.google.com/group/qiime-forum/browse_thread/thread/1f3e39e672faaacc
Salim
May 10, 2012, 9:19:53 PM5/10/12
to qiime...@googlegroups.com
Hi Antonio/Sean,
thank you for your prompt replies & assistance.
Antonio, You guessed right. Our servers here run CentOS5 or RHEL5.
I'll try your advices and report back.
Regards,
Salim
Migee
May 15, 2012, 11:02:23 AM5/15/12
to Qiime Forum
Hi all,
I have had the similar problem when trying to update to Qiime
1.5.0. I get following errors though. I tried to install libpgm,
libzmg1, and libzmq as SeanB had suggested, but couldnt find these
libraries in the standard repo's for OpenSuse.
Thank you
Migee
DEPLOYMENT SUMMARY
Packages deployed successfully:
Packages skipped (assumed successful):
data-lanemask, data-core, clearcut, raxml, ampliconnoise, cdbtools,
cytoscape, rtax, drisee, gg_otus, infernal, vienna, chimeraslayer,
python, mothur, fasttree, pplacer, blast, parsinsert, r, muscle,
rdpclassifier, uclust, cdhit, numpy, ipython, SQLAlchemy, tornado,
setuptools, mpi4py, biom-format, MySQL-python, pycogent, sphinx,
matplotlib, pprospector, pynast
Packages failed to deploy:
pyzmq, qiime
I have had the similar problem when trying to update to Qiime
1.5.0. I get following errors though. I tried to install libpgm,
libzmg1, and libzmq as SeanB had suggested, but couldnt find these
libraries in the standard repo's for OpenSuse.
Thank you
Migee
DEPLOYMENT SUMMARY
Packages deployed successfully:
data-lanemask, data-core, clearcut, raxml, ampliconnoise, cdbtools,
cytoscape, rtax, drisee, gg_otus, infernal, vienna, chimeraslayer,
python, mothur, fasttree, pplacer, blast, parsinsert, r, muscle,
rdpclassifier, uclust, cdhit, numpy, ipython, SQLAlchemy, tornado,
setuptools, mpi4py, biom-format, MySQL-python, pycogent, sphinx,
matplotlib, pprospector, pynast
Packages failed to deploy:
pyzmq, qiime
Antonio González Peña
May 15, 2012, 4:59:57 PM5/15/12
to qiime...@googlegroups.com
Hi Migee,
Can you edit the config file that you are using with app-deploy to
look like this in line 20:
log-level: DEBUG
run again the deploy and send us the errors you get?
Cheers
Can you edit the config file that you are using with app-deploy to
look like this in line 20:
log-level: DEBUG
run again the deploy and send us the errors you get?
Cheers
Migee
May 15, 2012, 6:37:24 PM5/15/12
to Qiime Forum
The debug text is huge, so i have just listed the steps with errors.
Let me know if you need to see the complete result.
Thanks
Migee
2012-05-15 18:33:12,366 - lib.util - INFO - Building pyzmq
2012-05-15 18:33:12,366 - lib.util - DEBUG - EXE: /data1/
qiime_software/python-2.7.1-release/bin/python setup.py build
2012-05-15 18:33:12,623 - lib.util - ERROR - Failed to
build pyzmq
2012-05-15 18:33:12,623 - lib.util - DEBUG - pyzmq build
failed, return code: 256
2012-05-15 18:33:12,623 - lib.util - DEBUG - Output:
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/zmq
copying zmq/__init__.py -> build/lib.linux-x86_64-2.7/zmq
creating build/lib.linux-x86_64-2.7/zmq/tests
copying zmq/tests/test_message.py -> build/lib.linux-x86_64-2.7/zmq/
tests
copying zmq/tests/test_error.py -> build/lib.linux-x86_64-2.7/zmq/
tests
copying zmq/tests/test_log.py -> build/lib.linux-x86_64-2.7/zmq/tests
copying zmq/tests/test_socket.py -> build/lib.linux-x86_64-2.7/zmq/
tests
copying zmq/tests/test_reqrep.py -> build/lib.linux-x86_64-2.7/zmq/
tests
copying zmq/tests/test_ioloop.py -> build/lib.linux-x86_64-2.7/zmq/
tests
copying zmq/tests/test_pair.py -> build/lib.linux-x86_64-2.7/zmq/tests
copying zmq/tests/test_monqueue.py -> build/lib.linux-x86_64-2.7/zmq/
tests
copying zmq/tests/test_stopwatch.py -> build/lib.linux-x86_64-2.7/zmq/
tests
copying zmq/tests/test_imports.py -> build/lib.linux-x86_64-2.7/zmq/
tests
copying zmq/tests/__init__.py -> build/lib.linux-x86_64-2.7/zmq/tests
copying zmq/tests/test_pubsub.py -> build/lib.linux-x86_64-2.7/zmq/
tests
copying zmq/tests/test_multipart.py -> build/lib.linux-x86_64-2.7/zmq/
tests
copying zmq/tests/test_device.py -> build/lib.linux-x86_64-2.7/zmq/
tests
copying zmq/tests/test_poll.py -> build/lib.linux-x86_64-2.7/zmq/tests
copying zmq/tests/test_zmqstream.py -> build/lib.linux-x86_64-2.7/zmq/
tests
copying zmq/tests/test_context.py -> build/lib.linux-x86_64-2.7/zmq/
tests
creating build/lib.linux-x86_64-2.7/zmq/utils
copying zmq/utils/strtypes.py -> build/lib.linux-x86_64-2.7/zmq/utils
copying zmq/utils/__init__.py -> build/lib.linux-x86_64-2.7/zmq/utils
copying zmq/utils/jsonapi.py -> build/lib.linux-x86_64-2.7/zmq/utils
creating build/lib.linux-x86_64-2.7/zmq/eventloop
copying zmq/eventloop/stack_context.py -> build/lib.linux-x86_64-2.7/
zmq/eventloop
copying zmq/eventloop/win32_support.py -> build/lib.linux-x86_64-2.7/
zmq/eventloop
copying zmq/eventloop/__init__.py -> build/lib.linux-x86_64-2.7/zmq/
eventloop
copying zmq/eventloop/zmqstream.py -> build/lib.linux-x86_64-2.7/zmq/
eventloop
copying zmq/eventloop/ioloop.py -> build/lib.linux-x86_64-2.7/zmq/
eventloop
creating build/lib.linux-x86_64-2.7/zmq/ssh
copying zmq/ssh/tunnel.py -> build/lib.linux-x86_64-2.7/zmq/ssh
copying zmq/ssh/__init__.py -> build/lib.linux-x86_64-2.7/zmq/ssh
copying zmq/ssh/forward.py -> build/lib.linux-x86_64-2.7/zmq/ssh
creating build/lib.linux-x86_64-2.7/zmq/devices
copying zmq/devices/monitoredqueuedevice.py -> build/lib.linux-
x86_64-2.7/zmq/devices
copying zmq/devices/basedevice.py -> build/lib.linux-x86_64-2.7/zmq/
devices
copying zmq/devices/__init__.py -> build/lib.linux-x86_64-2.7/zmq/
devices
creating build/lib.linux-x86_64-2.7/zmq/log
copying zmq/log/__init__.py -> build/lib.linux-x86_64-2.7/zmq/log
copying zmq/log/handlers.py -> build/lib.linux-x86_64-2.7/zmq/log
creating build/lib.linux-x86_64-2.7/zmq/core
copying zmq/core/__init__.py -> build/lib.linux-x86_64-2.7/zmq/core
copying zmq/utils/buffers.pxd -> build/lib.linux-x86_64-2.7/zmq/utils
copying zmq/utils/allocate.h -> build/lib.linux-x86_64-2.7/zmq/utils
copying zmq/utils/zmq_compat.h -> build/lib.linux-x86_64-2.7/zmq/utils
copying zmq/utils/pyversion_compat.h -> build/lib.linux-x86_64-2.7/zmq/
utils
copying zmq/devices/monitoredqueue.pxd -> build/lib.linux-x86_64-2.7/
zmq/devices
copying zmq/core/context.pxd -> build/lib.linux-x86_64-2.7/zmq/core
copying zmq/core/socket.pxd -> build/lib.linux-x86_64-2.7/zmq/core
copying zmq/core/message.pxd -> build/lib.linux-x86_64-2.7/zmq/core
copying zmq/core/libzmq.pxd -> build/lib.linux-x86_64-2.7/zmq/core
copying zmq/core/stopwatch.pxd -> build/lib.linux-x86_64-2.7/zmq/core
running build_ext
******************************************
Configure: Autodetecting ZMQ settings...
Custom ZMQ dir: None
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall
-Wstrict-prototypes -fPIC -Izmq/utils -Izmq/core -Izmq/devices -c
detect/vers.c -o detect/vers.o
detect/vers.c:3:17: error: zmq.h: No such file or directory
detect/vers.c: In function ‘main’:
detect/vers.c:7: warning: implicit declaration of function
‘zmq_version’
Fatal:
Failed to compile ZMQ test program. Please check to make sure:
* You have a C compiler installed
* A development version of Python is installed (including header
files)
* A development version of ZMQ >= 2.1.4 is installed (including
header files)
* If ZMQ is not in a default location, supply the argument --
zmq=<path>
* If you did recently install ZMQ to a default location,
try rebuilding the ld cache with `sudo ldconfig`
or specify zmq's location with `--zmq=/usr/local`
******************************************
2012-05-15 18:33:12,624 - lib.application - ERROR - Problem
building pyzmq.
2012-05-15 18:33:12,637 - lib.deploy - ERROR - Deploy of
pyzmq failed.
2012-05-15 18:33:19,720 - lib.util - INFO - Checking out
https://qiime.svn.sourceforge.net/svnroot/qiime/trunk
2012-05-15 18:33:19,720 - lib.util - DEBUG - EXE: svn co --
trust-server-cert --non-interactive https://qiime.svn.sourceforge.net/svnroot/qiime/trunk
/tmp/tmpeoCbFb/Qiime
2012-05-15 18:33:19,806 - lib.util - ERROR - svn checkout
failed: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk
2012-05-15 18:33:19,807 - lib.util - DEBUG - Output: svn:
invalid option: --trust-server-cert
Type 'svn help' for usage.
2012-05-15 18:33:19,807 - lib.application - ERROR - qiime download
failed.
2012-05-15 18:33:19,808 - lib.deploy - ERROR - Deploy of
qiime failed.
2012-05-15 18:33:19,856 - lib.application - DEBUG - Adding to
PYTHONPATH: /data1/qiime_software/pynast-1.1-release/lib/python2.7/
site-packages
2012-05-15 18:33:19,857 - lib.deploy - INFO - Deploy of
pynast skipped.
2012-05-15 18:33:19,867 - lib.application - DEBUG - Adding to
PYTHONPATH: /data1/qiime_software/pprospector-1.0.1-release/lib/
python2.7/site-packages
2012-05-15 18:33:19,868 - lib.deploy - INFO - Deploy of
pprospector skipped.
2012-05-15 18:33:49,870 - lib.util - INFO - Removing
directory: /data1/qiime_software/pyzmq-2.1.9-release
2012-05-15 18:33:49,871 - lib.util - INFO - Removing
directory: /data1/qiime_software/qiime-1.5.0-repository-3056
2012-05-15 18:33:49,872 - __main__ - DEBUG - Writing new
environment variables to activate.sh
Let me know if you need to see the complete result.
Thanks
Migee
2012-05-15 18:33:12,366 - lib.util - INFO - Building pyzmq
2012-05-15 18:33:12,366 - lib.util - DEBUG - EXE: /data1/
qiime_software/python-2.7.1-release/bin/python setup.py build
2012-05-15 18:33:12,623 - lib.util - ERROR - Failed to
build pyzmq
2012-05-15 18:33:12,623 - lib.util - DEBUG - pyzmq build
failed, return code: 256
2012-05-15 18:33:12,623 - lib.util - DEBUG - Output:
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/zmq
copying zmq/__init__.py -> build/lib.linux-x86_64-2.7/zmq
creating build/lib.linux-x86_64-2.7/zmq/tests
copying zmq/tests/test_message.py -> build/lib.linux-x86_64-2.7/zmq/
tests
copying zmq/tests/test_error.py -> build/lib.linux-x86_64-2.7/zmq/
tests
copying zmq/tests/test_log.py -> build/lib.linux-x86_64-2.7/zmq/tests
copying zmq/tests/test_socket.py -> build/lib.linux-x86_64-2.7/zmq/
tests
copying zmq/tests/test_reqrep.py -> build/lib.linux-x86_64-2.7/zmq/
tests
copying zmq/tests/test_ioloop.py -> build/lib.linux-x86_64-2.7/zmq/
tests
copying zmq/tests/test_pair.py -> build/lib.linux-x86_64-2.7/zmq/tests
copying zmq/tests/test_monqueue.py -> build/lib.linux-x86_64-2.7/zmq/
tests
copying zmq/tests/test_stopwatch.py -> build/lib.linux-x86_64-2.7/zmq/
tests
copying zmq/tests/test_imports.py -> build/lib.linux-x86_64-2.7/zmq/
tests
copying zmq/tests/__init__.py -> build/lib.linux-x86_64-2.7/zmq/tests
copying zmq/tests/test_pubsub.py -> build/lib.linux-x86_64-2.7/zmq/
tests
copying zmq/tests/test_multipart.py -> build/lib.linux-x86_64-2.7/zmq/
tests
copying zmq/tests/test_device.py -> build/lib.linux-x86_64-2.7/zmq/
tests
copying zmq/tests/test_poll.py -> build/lib.linux-x86_64-2.7/zmq/tests
copying zmq/tests/test_zmqstream.py -> build/lib.linux-x86_64-2.7/zmq/
tests
copying zmq/tests/test_context.py -> build/lib.linux-x86_64-2.7/zmq/
tests
creating build/lib.linux-x86_64-2.7/zmq/utils
copying zmq/utils/strtypes.py -> build/lib.linux-x86_64-2.7/zmq/utils
copying zmq/utils/__init__.py -> build/lib.linux-x86_64-2.7/zmq/utils
copying zmq/utils/jsonapi.py -> build/lib.linux-x86_64-2.7/zmq/utils
creating build/lib.linux-x86_64-2.7/zmq/eventloop
copying zmq/eventloop/stack_context.py -> build/lib.linux-x86_64-2.7/
zmq/eventloop
copying zmq/eventloop/win32_support.py -> build/lib.linux-x86_64-2.7/
zmq/eventloop
copying zmq/eventloop/__init__.py -> build/lib.linux-x86_64-2.7/zmq/
eventloop
copying zmq/eventloop/zmqstream.py -> build/lib.linux-x86_64-2.7/zmq/
eventloop
copying zmq/eventloop/ioloop.py -> build/lib.linux-x86_64-2.7/zmq/
eventloop
creating build/lib.linux-x86_64-2.7/zmq/ssh
copying zmq/ssh/tunnel.py -> build/lib.linux-x86_64-2.7/zmq/ssh
copying zmq/ssh/__init__.py -> build/lib.linux-x86_64-2.7/zmq/ssh
copying zmq/ssh/forward.py -> build/lib.linux-x86_64-2.7/zmq/ssh
creating build/lib.linux-x86_64-2.7/zmq/devices
copying zmq/devices/monitoredqueuedevice.py -> build/lib.linux-
x86_64-2.7/zmq/devices
copying zmq/devices/basedevice.py -> build/lib.linux-x86_64-2.7/zmq/
devices
copying zmq/devices/__init__.py -> build/lib.linux-x86_64-2.7/zmq/
devices
creating build/lib.linux-x86_64-2.7/zmq/log
copying zmq/log/__init__.py -> build/lib.linux-x86_64-2.7/zmq/log
copying zmq/log/handlers.py -> build/lib.linux-x86_64-2.7/zmq/log
creating build/lib.linux-x86_64-2.7/zmq/core
copying zmq/core/__init__.py -> build/lib.linux-x86_64-2.7/zmq/core
copying zmq/utils/buffers.pxd -> build/lib.linux-x86_64-2.7/zmq/utils
copying zmq/utils/allocate.h -> build/lib.linux-x86_64-2.7/zmq/utils
copying zmq/utils/zmq_compat.h -> build/lib.linux-x86_64-2.7/zmq/utils
copying zmq/utils/pyversion_compat.h -> build/lib.linux-x86_64-2.7/zmq/
utils
copying zmq/devices/monitoredqueue.pxd -> build/lib.linux-x86_64-2.7/
zmq/devices
copying zmq/core/context.pxd -> build/lib.linux-x86_64-2.7/zmq/core
copying zmq/core/socket.pxd -> build/lib.linux-x86_64-2.7/zmq/core
copying zmq/core/message.pxd -> build/lib.linux-x86_64-2.7/zmq/core
copying zmq/core/libzmq.pxd -> build/lib.linux-x86_64-2.7/zmq/core
copying zmq/core/stopwatch.pxd -> build/lib.linux-x86_64-2.7/zmq/core
running build_ext
******************************************
Configure: Autodetecting ZMQ settings...
Custom ZMQ dir: None
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall
-Wstrict-prototypes -fPIC -Izmq/utils -Izmq/core -Izmq/devices -c
detect/vers.c -o detect/vers.o
detect/vers.c:3:17: error: zmq.h: No such file or directory
detect/vers.c: In function ‘main’:
detect/vers.c:7: warning: implicit declaration of function
‘zmq_version’
Fatal:
Failed to compile ZMQ test program. Please check to make sure:
* You have a C compiler installed
* A development version of Python is installed (including header
files)
* A development version of ZMQ >= 2.1.4 is installed (including
header files)
* If ZMQ is not in a default location, supply the argument --
zmq=<path>
* If you did recently install ZMQ to a default location,
try rebuilding the ld cache with `sudo ldconfig`
or specify zmq's location with `--zmq=/usr/local`
******************************************
2012-05-15 18:33:12,624 - lib.application - ERROR - Problem
building pyzmq.
2012-05-15 18:33:12,637 - lib.deploy - ERROR - Deploy of
pyzmq failed.
2012-05-15 18:33:19,720 - lib.util - INFO - Checking out
https://qiime.svn.sourceforge.net/svnroot/qiime/trunk
2012-05-15 18:33:19,720 - lib.util - DEBUG - EXE: svn co --
trust-server-cert --non-interactive https://qiime.svn.sourceforge.net/svnroot/qiime/trunk
/tmp/tmpeoCbFb/Qiime
2012-05-15 18:33:19,806 - lib.util - ERROR - svn checkout
failed: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk
2012-05-15 18:33:19,807 - lib.util - DEBUG - Output: svn:
invalid option: --trust-server-cert
Type 'svn help' for usage.
2012-05-15 18:33:19,807 - lib.application - ERROR - qiime download
failed.
2012-05-15 18:33:19,808 - lib.deploy - ERROR - Deploy of
qiime failed.
2012-05-15 18:33:19,856 - lib.application - DEBUG - Adding to
PYTHONPATH: /data1/qiime_software/pynast-1.1-release/lib/python2.7/
site-packages
2012-05-15 18:33:19,857 - lib.deploy - INFO - Deploy of
pynast skipped.
2012-05-15 18:33:19,867 - lib.application - DEBUG - Adding to
PYTHONPATH: /data1/qiime_software/pprospector-1.0.1-release/lib/
python2.7/site-packages
2012-05-15 18:33:19,868 - lib.deploy - INFO - Deploy of
pprospector skipped.
2012-05-15 18:33:49,870 - lib.util - INFO - Removing
directory: /data1/qiime_software/pyzmq-2.1.9-release
2012-05-15 18:33:49,871 - lib.util - INFO - Removing
directory: /data1/qiime_software/qiime-1.5.0-repository-3056
2012-05-15 18:33:49,872 - __main__ - DEBUG - Writing new
environment variables to activate.sh
Antonio González Peña
May 15, 2012, 6:41:33 PM5/15/12
to qiime...@googlegroups.com
Hello again,
Not sure what to do with pyzmq but we can leave this one out because
is not a dependency for the general Qiime pipeline. Now about Qiime,
as you are installing the repository version and not the release
version you need to use svn but the svn in your system is pretty old
so you need to modify the config file by removing --trust-server-cert
from line 54 to make it look like this:
repository-options: --non-interactive
and redeploy.
Cheers.
Not sure what to do with pyzmq but we can leave this one out because
is not a dependency for the general Qiime pipeline. Now about Qiime,
as you are installing the repository version and not the release
version you need to use svn but the svn in your system is pretty old
so you need to modify the config file by removing --trust-server-cert
from line 54 to make it look like this:
repository-options: --non-interactive
and redeploy.
Cheers.
Migee
May 15, 2012, 7:01:41 PM5/15/12
to Qiime Forum
Hi Antonio,
I did it, but now i get following error and qiime fails to deploy. Am
i missing any other libraries? I had Qiime 1.4 working well in the
same system before.
Thanks
Migee
2012-05-15 18:58:09,461 - lib.util - ERROR - Failed to
install qiime
2012-05-15 18:58:09,461 - lib.util - DEBUG - qiime install
failed, return code: 256
2012-05-15 18:58:09,461 - lib.util - DEBUG - Output: ghc --
make -O2 FlowgramAli_4frame
Linking FlowgramAli_4frame ...
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/
ld: cannot find -lgmp
collect2: ld returned 1 exit status
make: *** [FlowgramAli_4frame] Error 1
cp FlowgramAli_4frame ../bin/
cp: cannot stat `FlowgramAli_4frame': No such file or directory
make: *** [install] Error 1
> > trust-server-cert --non-interactivehttps://qiime.svn.sourceforge.net/svnroot/qiime/trunk
> Research Assistant, ...
>
> read more »
I did it, but now i get following error and qiime fails to deploy. Am
i missing any other libraries? I had Qiime 1.4 working well in the
same system before.
Thanks
Migee
2012-05-15 18:58:09,461 - lib.util - ERROR - Failed to
install qiime
2012-05-15 18:58:09,461 - lib.util - DEBUG - qiime install
failed, return code: 256
2012-05-15 18:58:09,461 - lib.util - DEBUG - Output: ghc --
make -O2 FlowgramAli_4frame
Linking FlowgramAli_4frame ...
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/
ld: cannot find -lgmp
collect2: ld returned 1 exit status
make: *** [FlowgramAli_4frame] Error 1
cp FlowgramAli_4frame ../bin/
cp: cannot stat `FlowgramAli_4frame': No such file or directory
make: *** [install] Error 1
>
> read more »
Antonio González Peña
May 15, 2012, 7:06:14 PM5/15/12
to qiime...@googlegroups.com
Do you have ghc installed in your machine? You can test it like:
ghc --version
ghc --version
Migee
May 15, 2012, 7:24:36 PM5/15/12
to Qiime Forum
Hi Antonio,
Yup, I have it installed. Its the recent version (Glasgow Haskell
Compiler, Version 7.2.1, stage 2 booted by GHC version 6.12.1
). I had the same problem while installing the QIIME 1.4 (http://
groups.google.com/group/qiime-forum/browse_thread/thread/
a0600d7ab9fcb042/6e587988a96195bc?lnk=gst&q=migee#6e587988a96195bc),
and Jens suggested to install ghc 7.0.3 and it worked, but now i have
7.2.1.hmmm....()
Is there any way to skip the ghc?
Thanks
Migee
> ...
>
> read more »
Yup, I have it installed. Its the recent version (Glasgow Haskell
Compiler, Version 7.2.1, stage 2 booted by GHC version 6.12.1
). I had the same problem while installing the QIIME 1.4 (http://
groups.google.com/group/qiime-forum/browse_thread/thread/
a0600d7ab9fcb042/6e587988a96195bc?lnk=gst&q=migee#6e587988a96195bc),
and Jens suggested to install ghc 7.0.3 and it worked, but now i have
7.2.1.hmmm....()
Is there any way to skip the ghc?
Thanks
Migee
>
> read more »
Antonio González Peña
May 16, 2012, 6:44:31 PM5/16/12
to qiime...@googlegroups.com
Hi Migee,
You are right, ghc did some changes and they remove some libraries
from their newest release so now you have to do some extra steps to be
able to install Denoiser. In Ubuntu you will need to run these
commands, in OpenSuse only the first one should change but I'm not
certain about this:
sudo apt-get install cabal-install
cabal update
cabal install random
Cheers
You are right, ghc did some changes and they remove some libraries
from their newest release so now you have to do some extra steps to be
able to install Denoiser. In Ubuntu you will need to run these
commands, in OpenSuse only the first one should change but I'm not
certain about this:
sudo apt-get install cabal-install
cabal update
cabal install random
Cheers
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