Hi,
I plan to plot a sashimi plot to view the alternative splicing event of my
interested gene by using MISO.
After follow the following link,
http://genes.mit.edu/burgelab/miso/docs/and read through the forum.
Unfortunately, I still face some problems to run the complete set of MISO
successful.
On Thu, Mar 20, 2014 at 4:04 PM, Chia Jing Yi cjyxiao...@gmail.com wrote:
Hi,
I plan to plot a sashimi plot to view the alternative splicing event of my
interested gene by using MISO.
After follow the following link, http://genes.mit.edu/burgelab/miso/docs/and
read through the forum.
Hi,
Thanks a lot for your email.
I will upload the full traceback soon.
Sorry for posting the same thread at scipy-user too.
I don't aware about that numpy and scipy user group is linked.
I apologize for my mistakes.
I will be more careful in future.
best regards
Edge
On Fri, Mar 21, 2014
Thank you for pointing this out. Actually I tried both
--fcompiler=gnu95 and --fcompiler=gnu flags, but I got the same error
message.
As for the redhat version, I'm using Red Hat Enterprise Linux Server
release 6.3 (Santiago).
On Fri, Jul 6, 2012 at 12:42 AM, Paul Anton Letnes
However, I got the following error message:
error: Command /usr/bin/g77 -g -Wall -g -Wall -shared
build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/scipy/integrate/vodemodule.o
build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/fortranobject.o
-L/home/username/lib/ -L/usr/lib64
Link is a great suggestion! I was hesitating about whether or not to
paste such a long output.
The site.cfg file is shown in the following link.
https://gist.github.com/3059209
The output message for
$ python setup.py build --fcompiler=gnu95
can be found at the URL.
I usually find these problems by searching for error in the output, in
your case the complete problem is at the bottom of the log. The relocation
errors you're seeing are happening because the build process is trying to
link in Atlas libraries (located here: /home/hxc249/lib/atlas/lib/) that
were
Thank you. This is very helpful!
On Fri, Jul 6, 2012 at 6:23 AM, Aron Ahmadia a...@ahmadia.net wrote:
I usually find these problems by searching for error in the output, in
your case the complete problem is at the bottom of the log. The relocation
errors you're seeing are happening because
Dear all,
I've built blas, lapack, and atlas libraries, as shown below.
$ ls ~/lib/atlas/lib/
libatlas.a libcblas.a libf77blas.a liblapack.a libptcblas.a libptf77blas.a
The library location are specified by site.cfg file, as shown below.
[DEFAULT]
library_dirs =
Hi,
are you sure that you want g77 and not gfortran? If you want gfortran, you
should pass the
--fcompiler=gnu95
flag to setup.py.
Which redhat version are you building on? (I don't know red hat well enough to
comment, but perhaps someone else do...)
Paul
On 6. juli 2012, at 03:00,
Dear list,
I am having problems installing matplotlib (from source) and fipy.
I had installed numpy from source and it is running well:
:~$ python -c import numpy; print numpy.__version__
1.6.1
After being trying to solve this problem on matplotlib list, I was
recommended to ask numpy list.
I
On Sunday, March 18, 2012, ava...@famaf.unc.edu.ar wrote:
Dear list,
I am having problems installing matplotlib (from source) and fipy.
I had installed numpy from source and it is running well:
:~$ python -c import numpy; print numpy.__version__
1.6.1
After being trying to solve this
On Jul 24, 2010, at 3:08 PM, Benjamin Root wrote:
On Fri, Jul 23, 2010 at 10:10 AM, Jonathan Tu j...@princeton.edu wrote:
Hi,
I am trying to install Numpy on a Linux cluster running RHEL4. I installed a
local copy of Python 2.7 because RHEL4 uses Python 2.3.4 for various internal
On Sat 24/07/10 3:39 PM , David Cournapeau courn...@gmail.com wrote:
On Sun, Jul 25, 2010 at 4:23 AM, Jonathan Tu wrote:
On Jul 24, 2010, at 3:08 PM, Benjamin Root wrote:
On Fri, Jul 23, 2010 at 10:10 AM, Jonathan Tu wrote:
Hi,
I am trying to install Numpy on a Linux
On Sun, Jul 25, 2010 at 4:50 AM, Jonathan Tu j...@princeton.edu wrote:
I am unable to find the files lapack_lite.so or _dotblas.so. I used the
locate command to look for them.
If you just installed numpy, locate won't find them as locate uses a
database which is usually updated once in a
On Jul 24, 2010, at 4:04 PM, Keith Goodman wrote:
On Sat, Jul 24, 2010 at 12:58 PM, David Cournapeau courn...@gmail.com wrote:
On Sun, Jul 25, 2010 at 4:50 AM, Jonathan Tu j...@princeton.edu wrote:
I am unable to find the files lapack_lite.so or _dotblas.so. I used the
locate command to
On Sun, Jul 25, 2010 at 5:11 AM, Jonathan Tu j...@princeton.edu wrote:
On Jul 24, 2010, at 4:04 PM, Keith Goodman wrote:
On Sat, Jul 24, 2010 at 12:58 PM, David Cournapeau courn...@gmail.com
wrote:
On Sun, Jul 25, 2010 at 4:50 AM, Jonathan Tu j...@princeton.edu wrote:
I am unable to find
On Sun, Jul 25, 2010 at 5:13 AM, David Cournapeau courn...@gmail.com wrote:
On Sun, Jul 25, 2010 at 5:11 AM, Jonathan Tu j...@princeton.edu wrote:
On Jul 24, 2010, at 4:04 PM, Keith Goodman wrote:
On Sat, Jul 24, 2010 at 12:58 PM, David Cournapeau courn...@gmail.com
wrote:
On Sun, Jul 25,
It shows you don't use either atlas or even simple lapack. If your
install used atlas, the atlas libraries would show up on those .so
with ldd,
David
Hmm. Ok. What I did for Numpy installation was check out the source code
using svn. Then I did
python setup.py build
where I
On Sun, Jul 25, 2010 at 5:18 AM, Jonathan Tu j...@princeton.edu wrote:
It shows you don't use either atlas or even simple lapack. If your
install used atlas, the atlas libraries would show up on those .so
with ldd,
David
Hmm. Ok. What I did for Numpy installation was check out the source
Here is what I would do for RHEL4:
- use python 2.6, not 2.7, because the released numpy does not support 2.7
yet.
- build atlas 3.8.3 and lapack 3.1.1 by yourself: this is your core
issue here. Both lapack and atlas should be built with the -fPIC flag
on x86_64 arch (modify the make.inc in
On Jul 24, 2010, at 5:46 PM, Jonathan Tu wrote:
Here is what I would do for RHEL4:
- use python 2.6, not 2.7, because the released numpy does not support 2.7
yet.
- build atlas 3.8.3 and lapack 3.1.1 by yourself: this is your core
issue here. Both lapack and atlas should be built with the
On Sun, Jul 25, 2010 at 6:50 AM, Jonathan Tu j...@princeton.edu wrote:
Also, I recently tried this all again, only doing make shared, and only
using the list of libraries without pt. In both cases, when I ran Python
interactively and tried to load the numpy module, I got the following:
If you install shared libraries into a directory which is not looked
in by default by ld, you should add it to the LD_LIBRARY_PATH, e.g.:
LD_LIBRARY_PATH=$HOME/local/lib:$LD_LIBRARY_PATH python -c import numpy
David
Ok, that makes sense to me. I tried to see what the current value is by
On Sun, Jul 25, 2010 at 7:00 AM, Jonathan Tu j...@princeton.edu wrote:
If you install shared libraries into a directory which is not looked
in by default by ld, you should add it to the LD_LIBRARY_PATH, e.g.:
LD_LIBRARY_PATH=$HOME/local/lib:$LD_LIBRARY_PATH python -c import numpy
David
Ok,
On Jul 24, 2010, at 6:09 PM, David Cournapeau wrote:
On Sun, Jul 25, 2010 at 7:00 AM, Jonathan Tu j...@princeton.edu wrote:
If you install shared libraries into a directory which is not looked
in by default by ld, you should add it to the LD_LIBRARY_PATH, e.g.:
On Sat, Jul 24, 2010 at 3:12 PM, Jonathan Tu j...@princeton.edu wrote:
On Jul 24, 2010, at 6:09 PM, David Cournapeau wrote:
On Sun, Jul 25, 2010 at 7:00 AM, Jonathan Tu j...@princeton.edu wrote:
If you install shared libraries into a directory which is not looked
in by default by ld, you
On Sun, Jul 25, 2010 at 7:12 AM, Jonathan Tu j...@princeton.edu wrote:
What does that part do? It turns out that by fixing my library path, numpy
now imports. I assume that my installation of h5py doesn't need to be redone
just because I reinstalled Numpy?
Actually, you may have to if
On Jul 24, 2010, at 6:21 PM, David Cournapeau wrote:
On Sun, Jul 25, 2010 at 7:12 AM, Jonathan Tu j...@princeton.edu wrote:
What does that part do? It turns out that by fixing my library path, numpy
now imports. I assume that my installation of h5py doesn't need to be
redone just
On Sat, Jul 24, 2010 at 3:39 PM, Jonathan Tu j...@princeton.edu wrote:
On Jul 24, 2010, at 6:21 PM, David Cournapeau wrote:
On Sun, Jul 25, 2010 at 7:12 AM, Jonathan Tu j...@princeton.edu wrote:
What does that part do? It turns out that by fixing my library path, numpy
now imports. I
Yes, you should be worried. To run the numpy tests you need to install
nose. That's what your output said:
ImportError: Need nose = 0.10.0 for tests - see
http://somethingaboutorange.com/mrl/projects/nose
For h5py, you might want to try the h5py list. Did you remove the
build directory?
Hi,I am trying to install Numpy on a Linux cluster running RHEL4. I installed a local copy of Python 2.7 because RHEL4 uses Python 2.3.4 for various internal functionalities. I downloaded the Numpy source code usingsvn co http://svn.scipy.org/svn/numpy/trunk numpyand then I tried to build
sorry for the silly question: have you done
python setup.py install
from the numpy src directory, after untarring?
then cd out from the src directory and try to import numpy from python.
L.
On 7/31/07, kingshuk ghosh [EMAIL PROTECTED] wrote:
Hi,
I downloaded numpy1.0.3-2.tar and unzipped and
Hi,
I downloaded numpy1.0.3-2.tar and unzipped and untared.
However somehow new numpy does not work. It invokes
the old numpy 0.9.6 when i import numpy from python
and type in numpy.version.version .
I tried to change path and once I do that and when I do
import numpy it says
running from source
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