I've installed graphviz, following the command given here, to use it with Networkx
conda install -c alubbock pygraphviz
But there is a problem while trying to run the code given here
raise ValueError("Program %s not found in path." % prog)
ValueError: Program neato not found in path
I searched a bit and found Neato missing for 64 bit version.
Does this problem still exist? Is there a way to install Neato?
EDIT:
Following the instructions given below, I have installed Graphviz in the following folder
C:\Program Files (x86)\Graphviz2.38
Could someone suggest how to proceed from here?
import pygraphviz as pgv
doesn't work.
So I tried,
pip install pygraphviz
returns
pygraphviz/graphviz_wrap.c(2987): fatal error C1083: Cannot open include file: 'graphviz/cgraph.h': No such file or directory
error: command 'C:\\Program Files (x86)\\Microsoft Visual Studio 14.0\\VC\\BIN\\x86_amd64\\cl.exe' failed with exit status 2
----------------------------------------
ERROR: Failed building wheel for pygraphviz
Running setup.py clean for pygraphviz
Failed to build pygraphviz
Installing collected packages: pygraphviz
Running setup.py install for pygraphviz ... error
I'm not sure how to install pygraphviz now.
So the problem is that neato is missing.
As per your post seems like your system does not know where neato is. So add the directory where neato.exe is contained in to your PATH environment variable.
On Windows10, this can be done with Start -> Edit environment variables for your account -> select path in the window -> edit -> New -> C:\Program Files (x86)\Graphviz2.38\bin\
or whatever your install directory is.
Related
When I try to install Tensorflow this message appears. I use the latest version of python and pip.
ERROR: Could not install packages due to an OSError: [Errno 2] No such file or directory: 'C:\\Users\\julia\\AppData\\Local\\Packages\\PythonSoftwareFoundation.Python.3.9_qbz5n2kfra8p0\\LocalCache\\local-packages\\Python39\\site-packages\\tensorflow\\include\\external\\com_github_grpc_grpc\\src\\core\\ext\\filters\\client_channel\\lb_policy\\grpclb\\client_load_reporting_filter.h'
It appears on all the older versions of Tensorflow. On the newest release appears this:
ERROR: Could not find a version that satisfies the requirement tensorflow==1.2.0
ERROR: No matching distribution found for tensorflow==1.2.0
Try following this tutorial: https://www.howtogeek.com/266621/how-to-make-windows-10-accept-file-paths-over-260-characters/.
In my case, only deleting manually the "leftovers" of the package in the environment directory fixed this problem.
path : ... "\venv\Lib\site-packages\ {package name}"
make sure you backup before deleting any file.
Good day!
I'm trying to build MonoDevelop on/for an embedded/minimal Linux, and can't build msbuild from source which is why I'm using the binary from this DEB package.
This basically works as it seems, but now make ends with an error:
configure output
make output
Can someone please help me to get MonoDevelop built?
I see two errors in your build log:
/update/download/monodevelop-7.8/src/addins/VersionControl/MonoDevelop.VersionControl.Git/MonoDevelop.VersionControl.Git.csproj(146,5):
error MSB3073: The command "bash build_libgit2.sh" exited with code
-1.
"/update/download/monodevelop-7.8/Main.sln" (default target) (1) ->
"/update/download/monodevelop-7.8/external/fsharpbinding/MonoDevelop.FSharpBinding/MonoDevelop.FSharp.fsproj"
(default target) (81) ->
/update/download/monodevelop-7.8/external/fsharpbinding/MonoDevelop.FSharpBinding/MonoDevelop.FSharp.fsproj(33,3):
error MSB4019: The imported project
"/update/swroot/lib/mono/xbuild/Microsoft/VisualStudio/v15.0/FSharp/Microsoft.FSharp.Targets"
was not found. Confirm that the path in the declaration is
correct, and that the file exists on disk.
For the latter, did you install F#? (Just apt-get install fsharp should suffice.) And for the second, try running bash build_libgit2.sh separately to see the error message.
I currently am trying to build from Tensorflow 1.5 source because I am trying to implement a model on mobile and had to include some kernels. I have run through .configure in TF and I'm pointing at the 3.5 python location.
I am now trying to build the wheel file and for the life of me cannot get around the invalid command bdist_wheel error. I am currently at the step of building the wheel file using:
bazel-bin/tensorflow/tools/pip_package/build_pip_package /tmp/tensorflow_pkg
And I receive the following error:
Thu Feb 22 11:17:38 PST 2018 : === Using tmpdir: /tmp/tmp.XPe7Djtgg2
~/Documents/Git/tensorflow/bazel-bin/tensorflow/tools/pip_package/build_pip_package.runfiles
~/Documents/Git/tensorflow ~/Documents/Git/tensorflow
/tmp/tmp.XPe7Djtgg2 ~/Documents/Git/tensorflow Thu Feb 22 11:17:39 PST
2018 : === Building wheel usage: setup.py [global_opts] cmd1
[cmd1_opts] [cmd2 [cmd2_opts] ...] or: setup.py --help [cmd1 cmd2
...] or: setup.py --help-commands or: setup.py cmd --help
error: invalid command 'bdist_wheel'
I have also tried making sure wheel is installed but when I type:
sudo pip3 install wheel
I receive the following message.
Requirement already satisfied: wheel in
/usr/local/lib/python3.5/dist-packages
I went into my .bashrc file and have an entry for
export PYTHON_BIN_PATH=/usr/bin/
Now looking in build_pip_package I saw that it is using the line below to trigger the wheel build:
"${PYTHON_BIN_PATH:-python}" setup.py bdist_wheel ${PKG_NAME_FLAG} >/dev/null
At the path /usr/bin/ the symlink for python is for 2.7 which I think is the issue, because when I installed wheel using pip2, the wheel file built but it was for 2.7 and not 3.5 so it stated that it couldnt install the wheel file for the current environment.
I thought that maybe modifying the line above to the below entry would work but I still get the same bdist error. I cannot figure out how to get the wheel to build under 3.5.
"${PYTHON_BIN_PATH:-python3.5}" setup.py bdist_wheel ${PKG_NAME_FLAG} >/dev/null
I also tried setting an alias for python to python3.5 which works fine when I try to call just python at the command prompt but it does not work when it is being called from within the "build_pip_package" wheel building call.
Anyone know how I might be able to resolve this? I assume if I were to install conda I can probably get around this, but I would prefer not to have to deal with that if at all possible.
Thanks!
So I found what my issue was in this specific case. I initially performed the Tensorflow configure and wasn't aware of PYTHON_BIN_PATH at the time. now from reading, it seems that when I ran configure, it should have created this entry (at least from what I understand). This did not happen and it was only when I was dealing with the error stated above that I dug deeper and found that build_pip_package was accessing that variable and that it was not set in my .bashrc. It was at this time that I added the value and was trying to just run the building of the wheel.
After posting here, I then figured I would try rerunning through the full TF building process again and see if I could spot any other errors that I might have missed along the way. It was here that I then got an error stating that /usr/bin/ was a path which just happened to be the same value assigned to PYTHON_BIN_PATH. I modified it to export PYTHON_BIN_PATH=/usr/bin/python3 and then rebuilt tensorflow and once I finished I continued with building the wheel and installing it and all went through correctly.
Hopefully this helps someone at one point.
I am trying to install rpy2 package and getting following error both with
C:\python27>easy_install rpy2
Searching for rpy2
Reading http://pypi.python.org/simple/rpy2/
Reading http://rpy.sourceforge.net
Best match: rpy2 2.3.3
Downloading http://pypi.python.org/packages/source/r/rpy2/rpy2-2.3.3.tar.gz#md5=6cd95eb70645577cb53198ef0a32395e
Processing rpy2-2.3.3.tar.gz
Running rpy2-2.3.3\setup.py -q bdist_egg --dist-dir c:\users\chetan~1\appdata\local\temp\easy_install-wfxip9\rpy2-2.3.3\egg-di
st-tmp-rrezfb
"C:\PROGRA~2\R\R-28~1.0\bin\R" CMD config --ldflags
Invalid substring
in string
C:\Python27\lib\site-packages\setuptools\command\easy_install.py:921: RuntimeWarning: tp_compare didn't return -1 or -2 for ex
ception
raise DistutilsError("Setup script exited with %s" % (v.args[0],))
error: Setup script exited with Problem while running `"C:\PROGRA~2\R\R-28~1.0\bin\R" CMD config --ldflags`
And when I try pip this is what I get
c:\Python27\Lib\site-packages\django\bin>pip install rpy2
Downloading/unpacking rpy2
Running setup.py egg_info for package rpy2
"C:\PROGRA~2\R\R-28~1.0\bin\R" CMD config --ldflags
Invalid substring
in string
Problem while running `"C:\PROGRA~2\R\R-28~1.0\bin\R" CMD config --ldflags`
I spent a few days on this too... then I stumbled upon this thread, where a link is given: http://www.lfd.uci.edu/~gohlke/pythonlibs/#rpy2
On this page you can find (amongst other useful things) a pre-compiled version of rpy2 for Windows, and for different versions of Python. It apparently only works for R 2.15.3, I did not try it with other versions.
The error
"C:\PROGRA~2\R\R-28~1.0\bin\R" CMD config --ldflags
is probably caused by the absence of unix like tools in windows. (you might also have had an error like
'sh' is not recognized as an internal or external command, operable program or batch file
I finally got it to work on windows 7 by installing Rtools and mingw compiler and changing the setup.py and unixccompiler.py file. See rpy2 install on windows 7
Also the error
%load_ext rmagic
RuntimeError("Unable to locate R.dll within %s" % RHOME)
is caused by rpy2 not able to find R.dll correctly in the code. You can add R_HOME environment variable as eg C:\Program Files\R\R-3.0.2 the outside folder (for details see the link).
Hope this helps..
Recently had to attempt to build this from source. Got the rpy2-2.2.2 version so I can use with with Python 2.6.6 on Oracle Linux.
The solution to getting this to work was to fix a couple of things in the setup.py script.
First, allow get_rconfig() to allow empty strings. If there was a way to flag this, it wasn't obvious to me:
config = RConfig()
for about in ('--ldflags', '--cppflags',
'LAPACK_LIBS', 'BLAS_LIBS'):
#config += get_rconfig(r_home, about)
config += get_rconfig(r_home, about, allow_empty = True)
Secondly, fix a bug with the dropthrough in RConfig.from_string, where it was referencing a non-existent variable:
elif rconfig_m is None:
if allow_empty:
#if allow_empty and (rconfig == ''):
print(cmd + '\nreturned an empty string.\n')
This then allows the R CMD config loops to get parsed and the empty cases (which you will probably encounter if your R build was not built as a shared library) and I am able to complete the cycle with
python setup.py build install
I am having trouble getting PhantomJS and CasperJS working within the cygwin environment. I am very new to cygwin. I was able to download both packages for windows and run them via windows cmd.
To get them to work with Cygwin, I tried the following:
I downloaded the tar/zip files for both PhantomJS and CasperJS, I copied the contents on the "bin" folders into C:\cygwin\bin. But when I type in phantomjs on cygwin I get:
/usr/bin/phantomjs: cannot execute binary file
Then, I tried to do:
pip install git+git://github.com/ariya/phantomjs
but after waiting for a while I get the following response:
Downloading/unpacking git+git://github.com/ariya/phantomjs Cloning
git://github.com/ariya/phantomjs to /tmp/pip-dCF1oZ-build Running
setup.py egg_info for package from
git+git://github.com/ariya/phantomjs
Traceback (most recent call last):
File "", line 16, in
IOError: [Errno 2] No such file or directory: '/tmp/pip-dCF1oZ-build/setup.py'
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File "", line 16, in
IOError: [Errno 2] No such file or directory:
'/tmp/pip-dCF1oZ-build/setup.py'
---------------------------------------- Command python setup.py egg_info failed with error code 1 in /tmp/pip-dCF1oZ-build Storing
complete log in /home/tkondapalli/.pip/pip.log
Does any one have any advice on how to get this working? Does anyone use PhantomJS/CasperJS in the cygwin environment?
Also, I thought the .exe I am downloading and copying into the C:\cygwin\bin directory is the one for linux, so maybe that doesn't work? So this means that I need to compile from source on cygwin...
So, I started following directions for building phantomjs: http://phantomjs.org/build.html
The first thing we need to do is build OpenSSL for devel, but again I don't know how to do this for cygwin! So I just skipped this step for now, which is probably not right.
I did download the source from github and tried to build it. It failed with the follow error:
Makefile:217: recipe for target `qtemporaryfile.o' failed make: *
[qtemporaryfile.o] Error 1 make: * Waiting for unfinished jobs....
make: *** No targets specified and no makefile found. Stop.
./build.sh: line 90: src/qt/bin/qmake: No such file or directory
Earlier I had downloaded the executables for Linux, so it was not working. This time I downloaded the executables for windows and put it in C:/cygwin/bin, and it worked!
I don't understand why I would need to download the windows executable, when cygwin is a linux emulator. This confuses me, but at least it works now!
From the Cygwin website:
Cygwin is not: a way to run native Linux apps on Windows. You must rebuild your application from source if you want it to run on Windows.
Every applications needs to be rebuilt in order to be use on Windows (as it does not produce an elf file, but .exe file that requires the cygwin dll).
Nevertheless, the shell in cygwin can execute any windows's .exe file (such as ping, ipconfig, cmd, etc.), which is why you are able to run the windows version of PhantomJS under cygwin.
First, download and install Node.js from http://nodejs.org/download
Close and reopen Cygwin and type:
$ npm install -g phantomjs
$ npm install -g casperjs
Just ran into this issue, placing the phantomjs executable in C:/cygwin/bin solved everything. After that all you need to do is run the command C:/cygwin/bin/phantomjs to initialize the application.
Although Cygwin doesn't replace the standard cmd prompt, it is pretty useful!