Precisely the same as here, which hasn't been resolved.
Followed the sequential directions here; all channels added.
Tried:
Adding to .bash_profile export PKG_CONFIG_PATH=$PKG_CONFIG_PATH://anaconda/pkgs accordingly the directory where there is cairomm installed..
./configure -with--CAIROMM_CFLAGS -with--CAIROMM_LIBS
Can someone kindly make sure at least I have implemented alternate solutions correctly?
And of course I've tried the simplest conda install graph-tool after adding channels from ostrokach-forge and the like.
Instead of success, I get the following:
PackagesNotFoundError: The following packages are not available from current channels:
Whoa, so unpopular post!
For myself and other novices' use in the future ->
(after all, conda install-ed python is easier)
Slightly different but same in that certain library is not reached, acc. to this query:
conda needs to be able to find all the dependencies at once.
The -c flag only adds that channel for that one command.
conda install -c vgauthier rwest graph-tool. But an easier way is to add those channels to your configuration
conda config --add channels vgauthier --add channels rwest
And then perform
conda install graph-tool
But when I used conda install -c http://conda.anaconda.org/vgauthier graph-tool command, it worked instantly.
Before that, nothing worked. (when I only used the user name vguathier or ostrokach-forge or else)
If I type vi .condarc I see
channels:
- ostrokach-forge
- conda-forge
- defaults
And because I remain quite ignorant in using brew-installed packages with conda-installed python, I started out by following the directions to install all the necessary dependencies using brew. (including pixman)
Wonder how the command found everything though.. plus python upgraded to 3.6 from 3.5.
God this is how I am left with solving os issues.. i'm not 100 % clear how I made the computer connect the dots.
And still, nonetheless, I am still left with how to figure the install with ./configure. I want to understand the error msg that was returned and how to address it.
Related
conda doesn't find the module with the command conda install -c conda-forge/label/cf202003 websockets
and put's error:
Fetching package metadata: ......
Error: No packages found in current linux-armv7l channels matching: websockets
Did you mean one of these?
webassets, rb-em-websocket, pockets
You can search for this package on anaconda.org with
anaconda search -t conda websockets
From the "linux-armv7l" shown in the error, it appears that this is for an ARM-based platform, which is unfortunately not officially supported by any organization (e.g., Anaconda, Conda Forge, etc.), and one of the main community-contributed channels (rpi maintained by jjhelmus) for providing linux-armv7l-compatible package builds went inactive about 18 months ago. There is an open thread on the berryconda repo discussing its future and alternative options. In tragic summary: there is no channel that has a websockets package for this platform, hence the error.
As a side note, the additional labels that are provided when viewing a package on Anaconda Cloud (e.g., conda-forge/label/cf202003) have very specific purposes, and are rarely ever needed by most users (instead just use -c conda-forge). See the question, "Why are there multiple install commands on Anaconda Cloud?" for more details.
I am using conda version 4.5.11, python 3.6.6, and Windows 10.
I create a virtual environment using conda
conda create --name venv
When I check for installed packages
conda list
it is (as expected), empty.
But
pip list
is quite long.
Question #1: Why? - when I create a virtual environment using
python -m venv venv
the pip list is empty.
When I am not in an activated virtual environment, then
conda list
is also quite long, but it isn't the same as the pip list (* see follow up below)
In general, the pip list is a subset of the conda list. There is at least one exception ('tables' in the pip list, not in conda list) but I haven't analysed too closely. The conda list changes/displays some (all?) hyphens to underscores (or pip does the reverse). There also a few instances of versions being different.
Question #2: Why? (and follow up questions - can they be? and should I care?)
I was hoping to have a baseline conda 'environment' (that may not be the right word) -ie, the packages I have installed/updated into Ananconda/conda and then all virtual environments would be pulled from that. If I needed to install something new, it would be first installed into the baseline. Only when I need to create an application using different versions of packages from the baseline (which I don't envision in the foreseeable future) would I need to update the virtual environments differently.
Question #3: Am I overthinking this? I am looking for consistency and hoping for understanding.
-- Thanks.
Craig
Follow Up #1: After installing some packages to my empty conda venv, the results of conda list and pip list are still different, but the pip list is much shorter than it was, but is a subset of the conda list (it does not include two packages I don't use, so I don't care)
Follow Up #2: In the empty environment, I ran some code
python my-app.py
and was only mildly surprised that it ran without errors. As expected, when I installed a package (pytest), it failed to run due to the missing dependencies. So ... empty is not empty.
1. conda list vs pip list
If all you did was create the environment (conda create -n venv), then nothing is installed in there, including pip. Nevertheless, the shell is still going to try to resolve pip on using the PATH environment variable, and is possibly finding the pip in the Anaconda/Miniconda base environment.
2. pip list is subset of conda list outside env
This could simply be a matter of conda installing things other than Python packages, which pip doesn't have the option to install. Conda is a more generic package manager and brings in all the dependencies (e.g., shared libraries) necessary to run each package - by very definition this is a broader range than what is available from the PyPI.
3. Overthinking
I think this is more of a workflow style question, and generally outside the scope of StackOverflow because it's going to get opinionated answers. Try searching around for best practice recommendations and pick a style suited to your goals.
Personally, I would never try to install everything into my base/root Conda environment simply because the more one installs, the more one has dependency requirements pulling in different directions. In the end, Conda will centralize all packages anyway (anaconda/pkgs or miniconda3/pkgs), so I focus on making modular environments that serve specific purposes.
I am trying to install pysam.
After excecuting:
python path/to/pysam-master/setup.py build
This error is produced:
unable to execute 'x86_64-conda_cos6-linux-gnu-gcc': No such file or directory
error: command 'x86_64-conda_cos6-linux-gnu-gcc' failed with exit status 1
There are similar threads, but they all seem to address the problem assumig administriator rights, which I do not have. Is there a way around to install the needed files?
DISCLAIMER: This question derived from a previous post of mine.
manually installing pysam error: "ImportError: No module named version"
But since it might require a different approach, I made it a question of its own.
You can also receive the same error while installing some R packages if R was installed using conda (as I had).
Then just install the package by executing: conda install gxx_linux-64 to have that command available.
Source:
https://github.com/RcppCore/Rcpp/issues/770#issuecomment-346716808
It looks like Anaconda had a new release (4.3.27) that sets the C compiler path to a non-existing executable (quite an embarrassing bug; I'm sure they'll fix it soon). I had a similar issue with pip installing using the latest Miniconda, which I fixed by using the 4.3.21 version and ensuring I was not doing something like conda update conda.
See https://repo.continuum.io/miniconda/ which has release dates and versions.
It should now be safe to update conda. This is fixed in the following python packages for linux-64:
python-3.6.2-h0b30769_14.tar.bz2
python-2.7.14-h931c8b0_15.tar.bz2
python-2.7.13-hac47a24_15.tar.bz2
python-3.5.4-hc053d89_14.tar.bz2
The issue was as Jon Riehl described - we (Anaconda, formerly Continuum) build all of our packages with a new GCC package that we created using crosstool-ng. This package does not have gcc, it has a prefixed gcc - the missing command you're seeing, x86_64-conda_cos6-linux-gnu-gcc. This gets baked into python, and any extension built with that python goes looking for that compiler. We have fixed the issue using the _PYTHON_SYSCONFIGDATA_NAME variable that was added to python 3.6. We have backported that to python 2.7 and 3.5. You'll now only ever see python using default compilers (gcc), and you must set the _PYTHON_SYSCONFIGDATA_NAME to the appropriate filename to have the new compilers used. Setting this variable is something that we'll put into the activate scripts for the compiler package, so you'll never need to worry about it. It may take us a day or two to get new compiler packages out, though, so post issues on the conda-build issue tracker if you'd like to use the new compilers and need help getting started.
Relevant code changes are at:
py27: https://github.com/anacondarecipes/python-feedstock/tree/master-2.7.14
py35: https://github.com/anacondarecipes/python-feedstock/tree/master-3.5
py36: https://github.com/anacondarecipes/python-feedstock
The solution that worked for me was to use the conda to install the r packages:
conda install -c r r-tidyverse
or r-gggplot2, r-readr
Also ensure that the installation is not failing because of admin privileges.
It will save you a great deal of pain
After upgrading Golang to 1.19.1, I started to get:
# runtime/cgo
cgo: C compiler "x86_64-conda-linux-gnu-cc" not found: exec: "x86_64-conda-linux-gnu-cc": executable file not found in $PATH
Installing gcc_linux-64 from the same channel, has resolved it:
conda install -c anaconda gcc_linux-64
Somewhere in your $PATH (e.g., ~/bin), do
ln -sf $(which gcc) x86_64-conda_cos6-linux-gnu-gcc
Don't put this in a system directory or conda's bin directory, and remember to remove the link when the problem is resolved upstream. gcc --version should be version 6.
EDIT: I understand the sentiment in the comments against manipulating system paths, but maybe we can use a little critical thinking for the actual case in hand before reciting doctrine. What actually have we done with the command above? Nothing more than putting an executable (symlink) called x86_64-conda_cos6-linux-gnu-gcc in one's personal ~/bin directory.
If putting something in one's personal ~/bin directory broke future conda (after it fixes the C compiler path to point to gcc it embeds), then that would be a bug with conda. Would the existence of this verbosely named compiler mess with anything else? Unlikely either. Even if something did pick it up, it's just your system gcc after all...
This post summarize my painful but finally successful (just by chance) way to build own conda package for the
netgen meshing tool with Python interface. I found the recipe for the netgen build due to tpaviot.
After cloning the repository into 'netgen-conda' folder I ran:
conda build netgen-conda/netgen-6.2-dev
Which reports "Unsatisfiable dependencies": 'oce', 'gcc-5', 'binutils'.
So I tried to install these packages myself. Unfortunately the documentation do not emphasize the important fact that 'conda build' use its own temporary environment so it doesn't matter what you have installed (see). Nevertheless even installing 'gcc-5' together with 'binutils' manually turns out to be nearly impossible.
Hint for other newbies: Lot of my problems disappear after I learned details about channels.
First try was installing 'gcc-5' with 'binutils' from the 'salford_systems' channel suggested by anaconda:
conda install -c salford_systems binutils gcc-5
But it results in:
ERROR conda.core.link:_execute_actions(337): An error occurred while installing package 'salford_systems::gcc-5-5.3.0-0'.
LinkError: post-link script failed for package salford_systems::gcc-5-5.3.0-0
running your command again with-vwill provide additional information
location of failed script: /home/jb/miniconda3/envs/test/bin/.gcc-5-post-link.sh
Using verbose output ('-v') provides no more info. I was also confused by the fact that the script does not exist on the given path (probably automatically deleted).
With current experience I admit that the reason of problem can be dug out from the '-vv' output (reported issue). After some trying I found that only way to
install both is to first install 'gcc-5' into a clean environment and then install 'binutils'. Since 'conda build' installs everything
from scratch and there is no way to specify order of installed packages I was stuck.
Another issue that puzzled me is the 'conda build' long prefix hack. For unknown reason they use extremely long prefix for an auxiliary folder
which result in various kind of issues. I have faced to three such problems:
As is usual today, I have encrypted HOME causing a known issue.
Using a workaround '--croot /tmp' prevents creating the hard links from '/tmp' into 'HOME/miniconda3' since they are on different filesystems.
There is a fallback to use the copy. I even thought that the fallback doesn't work for a while, but it worked, just making the build running longer.
Trying to install 'gcc' (4.x) from 'default' channel complained about too short prefix. So ultimate workaroud was to set the length of the prefix manually
'--prefix-length 70'.
Finally, I found that the dependency on 'binutils' is not necessary and successfully build the package with:
conda build --prefix-length 70 -c salford_systems -c conda-forge -c dlr-sc netgen-conda/netgen-6.2-dev
Summary (of open questions):
Conda channels introduce a new kind of dependency hell already forgotten when using 'apt-get'. Is there a way to figure out what is a canonical channel for a package.
Does anyone succeed to build with combination 'gcc-5' and 'binutils'?
There is still lack of documentation about internal conda mechanisms and error messages do not provide clue to the problem.
Conda-build use a problematic prefix hack and lack ability to control order of installed packages. Does anybody know the reason for this hack?
Now TensorFlow is finally released on Windows, I have been trying to install it for the last 2 days, still no success. Need some help please.
After installing Anaconda 3, I followed the instructions here. But was not able to proceed further beyond activating the environment...
Just sorted things out...what a journey!! The solution is below:
So basically, we need to follow the process here. Also, you may get an error message like this:
Cannot remove entries from nonexistent file c:\users\george.liu\appdata\local\co
ntinuum\anaconda3\lib\site-packages\easy-install.pth
So, you just need to do this instead in Anaconda Prompt:
pip install --upgrade --ignore-installed https://storage.googleapis.com/tensorflow/windows/cpu/tensorflow-0.12.0rc0-cp35-cp35m-win_amd64.whl
This is due to a known bug as explained here.
Then you're all set. Enjoy!!