I use WSL2 and Desktop Container and my system is Windows 11. I create a container(the system used in the container is Ubuntu 20.04) and then connect the container with VSCode (remote docker). I have installed a miniconda in the container. But when I connected the container with VSCode, I can't use any conda commands. It seems that VSCode blocks the miniconda or doesn't recognize it. But I can use conda commands in this container if I access the container with "docker exec"(not with VSCode).
When I run "conda -h" in the VSCode, it shows the following information(conda does not work):
$ conda -h
bash: conda: command not found.
When I run "conda -h" in a container terminal(access with "docker exec"), it shows(conda works):
(base) root ➜ / $ conda -h
usage: conda [-h] [-V] command ...
conda is a tool for managing and deploying applications, environments and packages.
This problem may be similar to the problem which might cause by the VSCode while connecting a running container(VSCode does not launch Anaconda base Python).
But I have no idea why they happened.
Does anybody have any improvement to these problems? Thank you.
Python works all well in both cases.
The miniconda was installed into the Ubnutu system after I created the container. Is it the reason that VSCode does not recognize the conda commands?
I had problems with the same combination (vs code and anaconda) on Window 10.
In fact, there is a chance that you have to define your PATH variables for Anaconda and that it will work fine after that...
1. path\to\Anaconda\Scripts
2. path\to\Anaconda\Lib
3. path\to\Anaconda\
but it isn't the most elegant way. According to Anaconda the preferred way is working with a $PROFILE and $ENV VARIABLES
But on stackflow, are a lot of posts about similar problems I noticed:
Maybe in some of the comments you find your answer?
Conda: Creating a virtual environment
https://stackoverflow.com/questions/53137700/ssl-module-in-python-is-not-available-windows-7]
I hope you'll find it fast, probably something small and easy to change.
Like choosing the right terminal from VS Code or so...
Good luck!
I'm trying to apply the CyCADA paper: https://github.com/jhoffman/cycada_release/tree/8629c03fe78a72d4aaa0be1a434018f8600dfae4
I'm trying to run the "train_cycada.sh", but I get an error "No module named 'torch'", even though i have torch on my conda environment. I guess the problem is that bash on windows doesn't see the conda environment .... anyone know how to fix that?
While trying to install Perl modules like JSON::XS or YAML::XS, i receive the same error:
XS.xs:1:10: fatal error: 'EXTERN.h' file not found
I use MacBook, xCode is up to date, everything else that could help is up to date too.
Since OS X El Capitan, Apple introduced System Integrity Protection which restricts writing to /usr/lib /usr/bin and other sensitive directories (even to root or sudo user) that are used by the installation of Perl bundled with the Operating System. This can cause issues when it comes to installing new modules and also if trying to install XS modules ( those linked to external C libraries ).
For this reason you should not consider the default Perl installation as a working development environment, especially if you are installing custom modules.
Check out this thread on PM and others. I had since El-Capitan managed to solve this before by manually building from tarball and adding a few params or environment variables to set the paths believing that it would be best to retain use of the system Perl but this is not the way to go. This makes your environment difficult to build but also brittle and sensitive to OS updates that may either break things in many different ways.
The best practice seems to be starting with a Perl using brew install perl and work in this environment, remembering to setup your bash_profile as directed by the installer.
Also worth remembering to do a brew link perl. If you receive warnings about this clobbering what looks like system Perl libraries don't worry - these are likely modules that were installed by you over the top and it will cause you less trouble to link over these. If you have concerns, make a note of which module installs will be cleared and re-install them once your environment is configured ( ie your module installer approach is configured using cpanm or sticking with the old perl -MCPAN -e shell etc)
This new Perl setup from brew eliminates the need to continuing running sudo which adds another layer of things that can go wrong as environment variables don't follow through and permission conflicts arise etc.
Finally to simplify package/module installation I suggest doing a brew install cpanminus. If you had previously already installed this, you can ensure the paths etc are configured by doing a brew reinstall cpanminus
If you want to take it another step further then you can install perlbrew as well which will give you the ability to run multiple versions of Perl as your user and configure these with their own libs and modules which can be very useful particularly if aligning with your production environment for testing etc.
One problem you may face if moving from system Perl to this kind of approach is needing to deal with any hangovers from installing things with sudo. It wis worth taking a little time to get all this set up right though and your issues going forward will be greatly reduced and you won't be left with that nagging feeling that you don't want to change anything for fear of it all breaking.
I have also come across a Perl Blog Article that suggests a fix for XS issues with perlbrew on Mojave
This Gist described updating your cpan shell install root though this shouldn't be necessary unless your cpan is stuck in an old config after taking steps above.
I've also raised this as a new issue on PerlMonks
After reading https://developer.apple.com/documentation/xcode_release_notes/xcode_10_release_notes#3035624 and installing the Additional headers via
sudo installer -pkg /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg -target /
I successfully compiled without the missing 'EXTERN.h' error
In order to follow the common advice I also tried with Perlbrew to install a dedicated development version of Perl. Especially with the advice in mind First, do not use the system Perl on MacOS. The installed version is for Apple, not for you (see the discussion here: https://www.perlmonks.org/?node_id=1224727).
Unfortunately, the following error occurred:
Test Summary Report
-------------------
porting/libperl.t (Wstat: 65280 Tests: 35 Failed: 0)
Non-zero exit status: 255
Parse errors: No plan found in TAP output
Files=2653, Tests=1217766, 708 wallclock secs (52.74 usr 9.40 sys + 395.38 cusr 49.90 csys = 507.42 CPU)
Result: FAIL
make: *** [test_harness] Error 1
##### Brew Failed #####
Therefore, I decided to install it the following way (and not following the advice due to the error).
Even after having the above mentioned macOS SDK headers already installed on Catalina (macOS 10.15.2) it didn't work for me. I faced the issue during the installation of the Perl module Mac-SystemDirectory-0.13. The following steps (by identifying the missing file in hope of having a more generic approach for more or less equivalent issues) did the trick:
Locate the header file (in this case EXTERN.h)
sudo find /Library -type f -name EXTERN.h
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE/EXTERN.h
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/System/Library/Perl/5.28/darwin-thread-multi-2level/CORE/EXTERN.h
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE/EXTERN.h
Ensure the installed Perl version (here 5.18) match the header file:
perl -v | grep version
This is perl 5, version 18, subversion 4 (v5.18.4) built for darwin-thread-multi-2level
Export the path for the C-Compiler (note MacOSX10.15.sdk for Catalina and Perl Version 5.18)
export CPATH=/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE
Invoke the Makefile.PL with perl
perl Makefile.PL
BTW — For anybody who's still struggling with this, my workaround was:
bash% module="Sub::Util" # For example
bash% cpanm --configure-args="INC=-I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE" "$module"
Please try this
CPATH=$(dirname $(find /usr/local/Cellar/ -name EXTERN.h)) cpan JSON::XS
For Big Sur and perl 5.30, EXTERN.h is at /Library/Developer/CommandLineTools/SDKs/MacOSX11.3.sdk/System/Library/Perl/5.30/darwin-thread-multi-2level/CORE
I'm trying to upgrade CPAN itself and got that error. But I have /usr/bin/cpan and I can't write there so I have to tweak it to write the updated version to /usr/local/bin/cpan.
No promises, but yum install perl-devel worked for me.
As #huyz has helpfully pointed out, if you hit this error on a Mac, you don't have this option, even though this is probably your issue, and you need to follow one of the above methods of getting a version of Perl that isn't missing important chunks, as per other answers.
But if, dear reader, you hit this error on a linux host, as I did, then this might be an option for you.
Building on what E Lisse suggested, you might also have luck looking in
/System/Volumes/Data/Library/Developer/CommandLineTools/SDKs/
For example:
CPATH=$(dirname $(find /System/Volumes/Data/Library/Developer/CommandLineTools/SDKs/ -name EXTERN.h)) cpan JSON::XS
You could also find where EXTERN.h is located and add that to your shell by default, e.g. in your .bashrc or .zshrc file:
export CPATH=/System/Volumes/Data/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE/
I am trying to run algolia for the first time but it seems that there is something wrong with my environment. I followed the detailed explanation here https://community.algolia.com/jekyll-algolia/getting-started.html.
I installed and configured everything that is needed from the previous steps but when I run the command
ALGOLIA_API_KEY=xxxxxxxxxxxxxx bundle exec jekyll algolia
I get an error:
'ALGOLIA_API_KEY' is not recognized as an internal or external command,
operable program or batch file.
I have been rereading the documentation for both jekyll and angolia but couldn't find anything that could be helpful.
Since you're running on Windows, you cannot set an environment variable for your command like you can do on UNIX.
As advised in this question, Setting and using variable within same command line in Windows cmd.exe, I believe you could use
set ALGOLIA_API_KEY=xxxxxxxxxxxxxx && bundle exec jekyll algolia
I want to import and use dataset package of python at AWS Lambda. The dataset package is about MySQL connection and executing queries. But, when I try to import it, there is an error.
"libmysqlclient.so.18: cannot open shared object file: No such file or directory"
I think that the problem is because MySQL client package is necessary. But, there is no MySQL package in the machine of AWS Lambda.
How to add the third party program and how to link that?
You should install your packages in your lambda folder :
$ pip install YOUR_MODULE -t YOUR_LAMBDA_FOLDER
And then, compress your whole directory in a zip to upload in you lambda.
What you have to do is to include the binaries needed with your lambda package.
You need to utilize pip and create an isolated environment.Your zip uploaded to lambda needs to have the python2.7/site-packages included (the ones installed with pip).
Now there are extreme cases of os-related dependencies.
This has a tricky solution.
In those cases you have to spawn an amazon linux ec2 instance in order to build/get those dependencies and package them with your lambda.
Once your lambda is packaged you can close the ec2 instance.
Check this guide if virtualenv is not enough.
This is an os dependent system file. I'm guessing that you successfully installed the Python mysql client, but you still need the system mysql client, which seems to be a different version on your system than the lambda one. While building your virtual environment on the official lambda image will definitely fix this problem, you might have some luck copying your own copy of this system file into your lambda zip file.
I found mine with
locate libmysqlclient.so.18
Note: depending on your system, the version number at the end might be different. Use the version in the error you receive.
Adding that file on the top level of my zip file with
cd \path\from\locate\to\libmysqlclient
followed by
zip -u \path\to\lambda\zip\file.zip libmysqlclient.so.18
worked for me.