I have been trying to install obspy and have been running into a lot of problems. I want to install obspy which has a dependency on pyproj. But apparently obspy only works with pyproj 1.9.5.1, which I tried installing using pip (pip3 install pyproj==1.9.5.1), but only got the errors like-
_proj.c:7488:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
Digging deeper I found that it might be a Cython problem, and installing pyproj directly from github might help, because it would apparently make Cython recompile all the necessary files. Something along the lines of -
pip3 install git+https://github.com/jswhit/pyproj.git
However this one gives the error -
ERROR: Minimum supported proj version is 6.2.0, installed version is 5.2.0.
I di try installing a higher version of libproj-dev (sudo apt install libproj-dev=6.2.0) however it shows that there is no candidate for 6.2.0. I tried downloading the deb file and installing from that using -
sudo apt-get install ~/Downloads/libproj-dev_6.2.0-1_amd64.deb
which just leads to the error -
The following packages have unmet dependencies:
libproj-dev : Depends: libproj15 (= 6.2.0-1) but it is not installable
E: Unable to correct problems, you have held broken packages.
But I think this is not the right way to install for me anyway, since I need a specific version. Hence I tried installing directly from the tarball of the release -
pip3 install https://github.com/pyproj4/pyproj/archive/v1.9.5.1rel.tar.gz
Which leads to the first error I had, evidently due to Cython.
With errors on everything I tried to do to fix this, I am not sure what even is relevant to my problem now.
Any help is appreciated, and if this site is not the correct place for this question, please help me migrate it to its proper destination.
I am on Ubuntu 18.10.
The problem is, that Cython-generated c-files don't work for Python-3.7 if generated with Cython versions up to 0.27.3 (at least): The setup.py of pyproj (at least in the version 1.9.5.1) doesn't regenerate the_proj.c, which is generated with Cython 0.23.2 and thus the installation cannot succeed.
You have the following options:
stay on Python3.6 where everything works out of the box.
regenerate _proj.c with a current Cython-version.
For the second option:
download and unzip your prefered version from https://github.com/pyproj4/pyproj/releases/tag/v1.9.5.1rel and switch to the created folder pyproj-1.9.5.1rel.
check, that the cython-version is >=0.27.3. via cython --version.
regenerate the _proj.c file via cython -3 _proj.pyx (_proj.pyx looks like Python3-code, but also language_level=2 (i.e. cython -2 _proj.pyx) will probably work.
install running pip install .
pyproj 1.9.5.1 was release at Jan 7, 2016. At that time, the latest version Python was 3.5. In my tests. pyproj 1.9.5.1 failed to be installed on Python 3.7.4, but succeeded on Python 3.5.7.
You need to create a environment with Python 3.5 by pyenv or conda.
References
pyproj 1.9.5.1 release
Python release history
Related
Suddenly pip cant install or find any package, it cant even figure out its own version.
I reinstalled python multiple times, i have the latest version of python 3 and pip. I also tried to clear pip cache. Nothing works, this is really annoying...
Errors:
>pip install redblacktree
ERROR: Could not find a version that satisfies the requirement redblacktree (from versions: none)
ERROR: No matching distribution found for redblacktree
WARNING: There was an error checking the latest version of pip
>pip config list
freeze.user='yes'
global.index-url='http://pypi.org/simple'
global.trusted-host='pypi.org'
install.user='yes'
list.user='yes'
uninstall.user='yes'
I fixed it by locating the pip.ini config file and removing the line index-url = http://pypi.org/simple
Recently I have been installed Python 3.8.2 ( Feb 24, 2020) (64bit, Windows). Afterward, I've been updated Pip 20.0.2. And then trying to install Unittest" pip install unittest" but unfortunately it's appearing this message.
Does anyone has been faced this same problem?
C:\Users\BiploB>pip install unittest --user
WARNING: pip is being invoked by an old script wrapper. This will fail in a future version of pip.
Please see https://github.com/pypa/pip/issues/5599 for advice on fixing the underlying issue.
To avoid this problem you can invoke Python with '-m pip' instead of running pip directly.
ERROR: Could not find a version that satisfies the requirement unittest (from versions: none)
ERROR: No matching distribution found for unittest
enter link description here
If I am not mistaken unittest is part of Python's standard library. Meaning, it's available per default, meaning there is no need (and also no way) to install separately.
I'm trying to install the package "Tax4Fun" but keep failing.
I've tried 2 different ways:
install.packages("devtools")
devtools::install_url("http://tax4fun.gobics.de/Tax4Fun/Tax4Fun_0.3.1.tar.gz")
library(Tax4Fun)
The error that I get is:
ERROR: dependency 'biom' is not available for package 'Tax4Fun'
I've also tried installing biom directly
BiocManager::install("biom")
which does not work either
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05)
Installing package(s) 'biom'
Installation path not writeable, unable to update packages: boot, foreign, KernSmooth,
mgcv, nlme, survival
Warning message:
package ‘biom’ is not available (for R version 3.6.1)
The other way I've tried to install Tax4Fun directly is
BiocManager::install("Tax4Fun")
I get the following error code:
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05)
Installing package(s) 'Tax4Fun'
Installation path not writeable, unable to update packages: boot, foreign, KernSmooth,
mgcv, nlme, survival
Warning message:
package ‘Tax4Fun’ is not available (for R version 3.6.1)
Please help :)
You need to install it by downloading the packages from source (http://tax4fun.gobics.de). Then it depends whether you are running on Linux/Mac or Windows.
From the command line, you navigate to the folder containing the .tar.gz downloaded package. Then you should install it using:
R CMD INSTALL Tax4Fun_0.3.1.tar.gz
But dependancies are not installed by default. So you need to install dependancies manually, Qiimer and Biom, which are both deprecated on Cran. You install them using the same command, after you have downloaded the packages from the Cran archives.
Before that, you need to also install their dependancies in R:
install.packages("pheatmap")
install.packages("RJSONIO")
Then you should be able to proceed as mentioned above: install Qiimer and Biom from the command line first. Then Tax4Fun from the command line too.
If you are running on Windows you should have quite the same issues, but the installation of the different packages and dependancies is different. You can have a look at the readme at http://tax4fun.gobics.de
I'm working on a project which was written in Python 2, and I'm upgrading it to Python 3. So far, I've just been finding minor syntax errors which are easily fixable. What I've done is created a new project in Python 3, ensured that it worked, and copies chunks of code from the old project into the new one.
Right now, I'm having trouble with pysvn. Initially, I was getting this error:
ImportError: No module named 'pysvn'
At this point, I tried using pip install pysvn, which didn't work. I got the following:
pip install pysvn
Collecting pysvn
Could not find a version that satisfies the requirement pysvn (from versions:)
No matching distribution found for pysvn
So then after a bit of research, I went to the pysvn download site and tried:
>pip install --index-url http://pysvn.tigris.org/project_downloads.html pysvn, which gave me this error:
Collecting pysvn
The repository located at pysvn.tigris.org is not a trusted or secure host and is being ignored. If this repository is available via HTTPS it is recommended to use HTTPS instead, otherwise you may silence this warning and allow it anyways with '--trusted-host pysvn.tigris.org'.
and also the same error as when I tried >pip install pysvn.
My next step was to manually download the .exe file for the version I needed, and I was able to successfully install pysvn. I have checked the site-packages directory, and pysvn is indeed there, but pip still can't tell me anything about it:
>pip show pysvn
>
When I do this for another installed module, selenium for example, I get the following:
pip show selenium
Metadata-Version: 1.1
Name: selenium
Version: 2.49.2
Summary: Python bindings for Selenium
Home-page: https://github.com/SeleniumHQ/selenium/
Author: UNKNOWN
Author-email: UNKNOWN
License: UNKNOWN
Location: ...\lib\site-packages
Requires:
I was able to verify that the installation of pysvn was successful because my project now runs instead of giving me that ImportError.
So why can pip not give me information for another module in the same directory that was successfully installed?
As it turns out, because I didn't use pip install for pysvn, pip didn't know that pysvn existed. Because it wasn't available from PyPI (the Python Package Index), there was no way that pip could see it (because that's where pip goes first to find packages that it's attempting to install).
From the pip user guide:
pip supports installing from PyPI, version control, local projects, and directly from distribution files.
Since I had eventually downloaded pysvn from its own download site (which was not any of the above 4 options) and ran the .exe manually, pip simply doesn't know about it even though it's in the same directory as other packages installed by pip.
I suppose I could've also retrieved the distribution files and used pip with those, but my workaround did the trick.
My way on linux:
Get sources from here
tar -zxf pysvn-1.9.10.tar.gz
apt-get install subversion libsvn1 libsvn-dev make g++
cd pysvn-1.9.10/Source
python setup.py configure --pycxx-dir=/pysvn-1.9.10/Import/pycxx-7.1.3/
make
Here i've got errors below:
Compile: /pysvn-1.9.10/Import/pycxx-7.1.3/Src/cxxsupport.cxx into cxxsupport.o
/pysvn-1.9.10/Import/pycxx-7.1.3/Src/cxxsupport.cxx:42:10: fatal error: Src/Python3/cxxsupport.cxx: No such file or directory
#include "Src/Python3/cxxsupport.cxx"
Compile: /pysvn-1.9.10/Import/pycxx-7.1.3/Src/cxxextensions.c into cxxextensions.o
/pysvn-1.9.10/Import/pycxx-7.1.3/Src/cxxextensions.c:42:10: fatal error: Src/Python3/cxxextensions.c: No such file or directory
#include "Src/Python3/cxxextensions.c"
It is needed to edit that files:
vi /pysvn-1.9.10/Import/pycxx-7.1.3/Src/cxxsupport.cxx
change #include "Src/Python3/cxxsupport.cxx" to
#include "Python3/cxxsupport.cxx"
and same on second file. Than make again:
make clean && make
...
Compile: /code/pysvn-1.9.10/Import/pycxx-7.1.3/Src/cxxextensions.c into cxxextensions.o
Compile: /code/pysvn-1.9.10/Import/pycxx-7.1.3/Src/IndirectPythonInterface.cxx into IndirectPythonInterface.o
Compile: /code/pysvn-1.9.10/Import/pycxx-7.1.3/Src/cxx_exceptions.cxx into cxx_exceptions.o
Link pysvn/_pysvn_3_7.so
Then just copy it to the site-packages (change to yours directory):
mkdir /usr/local/lib/python3.7/site-packages/pysvn
cp /code/pysvn-1.9.10/Sources/pysvn/__init__.py /usr/local/lib/python3.7/site-packages/
cp /code/pysvn-1.9.10/Sources/pysvn/_pysvn*.so /usr/local/lib/python3.7/site-packages/
Hello stack community!
I'm not sure if my question is graph-tool related or gtk-related, but maybe both. Moreover, sorry if what I did while trying to solve it is plain stupid, I'm not a programmer by formal education, so I know just as much as I could find by google and comprehend.
Here is the problem:
After I brew install graph-tool, launch python and try to import graph_tool.all I get the following error:
/usr/local/lib/python2.7/site-packages/graph_tool/draw/cairo_draw.py:1318: RuntimeWarning: Error importing Gtk module: No module named repository; GTK+ drawing will not work.
Previously I was sure that if import pygtk; pygtk.require('2.0'); import gtk works, that means the error is a graph-tool issue, but that don't have to be the case since graph-tool might use gtk (3??) and GObject (right?) and the upper checks for gtk2 and pygtk ( This question led me to this thought ).
I tried reinstalling gtk, GObject and all dependencies. Wipe all brew-related and brew itself and then reinstall everything (as in here). Still same error appears. I also tried to unlink everything from brew and link it again just to be sure, but this does not change anything either.
What else did I check:
I'm running MAC OS X Version 10.10.3, homebrew-installed python 2.7.10 (python --version returns Python 2.7.10 which is the one installed by brew; which python points to /usr/local/bin/python). brew info graph-tool shows that all requirements of it are there (even the optional ones). GTK 2.24.28, GTK+3 3.16.4, PyGobject 2.28.6, GObject-introspection 2.28.6, Cairo 1.14.2, Py2Cairo 1.10.0, pango 1.36.8, XQuartz 2.7.7 etc are installed, dependencies of those are fine as well. gi 1.2 is installed (via pip), gi.repository is indeed not there. I am aware of this question, but I have PyGObjects installed.
I also read this question and the reply, but none of this solves my problem as far as I can judge.
I've spend two days looking for the solution, so any help is appreciated.
It's seem to be a cairo dependency issue.
As you may see here, graph-tool package require a lot of depencies (numpy, gfortran, scipy, freetype, libpng, matplotlib, boost, cgal, graphviz, cairo, cairomm, py2cairo)
In your case you may probably solve the issue with a clean reinstall of "cairo".
Try those commands:
brew install cairo
brew install cairomm
brew install py2cairo
If "brew" ask you to run command or install other packages, do it !
(We assume here that "brew" is properly installed)
Best regards
I've faced the same issue (with a slight difference on the line number):
>>> from graph_tool.all import *
/usr/local/lib/python2.7/site-packages/graph_tool/draw/cairo_draw.py:1499: RuntimeWarning: Error importing Gtk module: No module named gi; GTK+ drawing will not work.
warnings.warn(msg, RuntimeWarning)
I know it's a relatively old question but wanted to share how I did it. You said you tried reinstalling GObject, but that is what made it work here.
I followed the installing instructions
brew install pygobject3 --with-python#2 gtk+3
which said gtk+3 and pygobject3 were already installed. Then I ran:
brew reinstall gtk+3
and
brew upgrade pygobject3
which made the import work.