I am trying to build and deploy this bookdown project with GitHub Actions. One of the chapters uses the keras R package, which means I need to install Conda (or set up a virtual environment). At the end of the Miniconda installation command, there is an error when trying to collect metadata.
2020-06-24T04:47:59.7495480Z * Miniconda has been successfully installed at '/Users/runner/Library/r-miniconda'.
2020-06-24T04:47:59.7496060Z [1] "/Users/runner/Library/r-miniconda"
2020-06-24T04:48:00.3909040Z * Project '~/runners/2.263.0/work/drake/drake' loaded. [renv 0.10.0]
2020-06-24T04:48:00.7964920Z * The project and lockfile are out of sync -- use `renv::status()` for more details.
2020-06-24T04:48:00.7968340Z Warning message:
2020-06-24T04:48:00.7969190Z Project requested R version '3.6.0' but '4.0.1' is currently being used
2020-06-24T04:48:05.2408080Z Collecting package metadata (current_repodata.json): ...working... failed
2020-06-24T04:48:05.2410390Z
2020-06-24T04:48:05.2410820Z NotWritableError: The current user does not have write permissions to a required path.
2020-06-24T04:48:05.2411080Z path: /usr/local/miniconda/pkgs/cache/b89cf7bf.json
2020-06-24T04:48:05.2411230Z uid: 501
2020-06-24T04:48:05.2411350Z gid: 20
2020-06-24T04:48:05.2411430Z
2020-06-24T04:48:05.2411690Z If you feel that permissions on this path are set incorrectly, you can manually
2020-06-24T04:48:05.2411940Z change them by executing
2020-06-24T04:48:05.2412010Z
2020-06-24T04:48:05.2412260Z $ sudo chown 501:20 /usr/local/miniconda/pkgs/cache/b89cf7bf.json
2020-06-24T04:48:05.2412330Z
2020-06-24T04:48:05.2413470Z In general, it's not advisable to use 'sudo conda'.
2020-06-24T04:48:05.2413570Z
2020-06-24T04:48:05.2414250Z
2020-06-24T04:48:05.2886400Z ##[error]Error: Error 1 occurred creating conda environment r-reticulate
2020-06-24T04:48:05.2890770Z Execution halted
2020-06-24T04:48:05.3050700Z ##[error]Process completed with exit code 1.
The full job log is here.
Depending on how R is set up, this post might be helpful for you. You might need to configure the .Renviron file.
Unable to change python path in reticulate (R)
Related
after installing all prerequietsed/environment when i am trying to install Repositary Strain Package Showing this error: 'strain': not a valid cloud name. Must be one of ['folsom','folsom-proposed','grizzly','grizzly-proposed', 'havana', 'havana-proposed', 'icehouse', 'icehouse-proposed', 'juno', 'juno-proposed', 'octa', 'octa-proposed', 'newton', 'newton-proposed',
i have try to install that package removing and recreating another VM and follow the instruction page -- openstack, but still same issue their.
i want the points which i need to check which is responsible for giving following error.
Here's what I'm doing:
I have a blog that uses blogdown to render .Rmd files.
Some of the code snippets in the blog are in Python. I'm using reticulate for that.
I'm using a GitHub workflow to build and publish the blog as part of a larger website. This workflow sets up the environment and package dependencies in miniconda.
The last time this ran was six months ago. At that time, it worked. Now, it does not. I can't seem to replicate the behavior locally for more detailed debugging.
It seems to be trying to put a mamba command into normalizePath instead of a filesystem path (www-main is the name of the repository):
conda activate www-main
Rscript -e 'blogdown::build_site(local=FALSE, run_hugo=FALSE, build_rmd="content/blog/2020-08-28-api.Rmd")'
shell: /usr/bin/bash -l {0}
env:
CONDA_PKGS_DIR: /home/runner/conda_pkgs_dir
Rendering content/blog/2020-08-28-api.Rmd...
[...]
Quitting from lines 401-410 (2020-08-28-api.Rmd)
Error in normalizePath(conda, winslash = "/", mustWork = TRUE) :
path[1]="# cmd: /usr/share/miniconda/condabin/mamba update --name www-main --file /home/runner/work/www-main/www-main/conda": No such file or directory
Calls: local ... python_munge_path -> get_python_conda_info -> normalizePath
Execution halted
Error: Failed to render content/blog/2020-08-28-api.Rmd
Execution halted
Lines 401-410 of 2020-08-28-api.Rmd are a Python code block:
400 ```{python python-data, dev='svg'}
401 import covidcast
402 from datetime import date
403 import matplotlib.pyplot as plt
404
405 data = covidcast.signal("fb-survey", "smoothed_hh_cmnty_cli",
406 date(2020, 9, 8), date(2020, 9, 8),
407 geo_type="state")
408 covidcast.plot_choropleth(data, figsize=(7, 5))
409 plt.title("% who know someone who is sick, Sept 8, 2020")
410 ```
The useful bits of the output of conda info, in case it helps:
active environment : www-main
active env location : /usr/share/miniconda/envs/www-main
shell level : 1
user config file : /home/runner/.condarc
populated config files : /home/runner/.condarc
conda version : 4.12.0
conda-build version : not installed
python version : 3.9.12.final.0
virtual packages : __linux=5.15.0=0
__glibc=2.31=0
__unix=0=0
__archspec=1=x86_64
base environment : /usr/share/miniconda (writable)
conda av data dir : /usr/share/miniconda/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /home/runner/conda_pkgs_dir
envs directories : /usr/share/miniconda/envs
/home/runner/.conda/envs
platform : linux-64
user-agent : conda/4.12.0 requests/2.27.1 CPython/3.9.12 Linux/5.15.0-1020-azure ubuntu/20.04.5 glibc/2.31
UID:GID : 1001:121
netrc file : None
offline mode : False
I found this, but their workaround doesn't make sense for me since I'm not using papermill: https://github.com/rstudio/reticulate/issues/1184
I found this, but my paths don't have spaces: https://github.com/rstudio/reticulate/issues/1149
I found this, but their problem includes an entirely reasonable value for path[1], unlike mine: How can I tell R where the conda environment is via a docker image?
The build environment for this is a bit of a bear but I can probably put together a minimum working (/nonworking) example if needed, lmk
I tracked this down to at least two bits of weird/buggy behavior in reticulate and found a workaround: switch from vanilla miniconda to Mambaforge.
The TL;DR seems to be that whatever wacky ubuntu-latest setup-miniconda#v2 environment started putting into meta/history doesn't include a create line, which is what reticulate needs in order to figure out which conda goes with which python, because (1) it ignores the reticulate.conda_binary setting for some reason, and (2) it uses a more restrictive regex to parse the lines of the history file than the regex it uses to select them. Mambaforge does include the create line, so reticulate is happy.
- uses: conda-incubator/setup-miniconda#v2
with:
python-version: 3.9
activate-environment: www-main
miniforge-variant: Mambaforge
miniforge-version: latest
use-mamba: true
use-only-tar-bz2: true # (for caching support)
- name: Update environment
run: mamba env update -n www-main -f environment.yml
I have a Plone 5.0.5 deployment and the need the package zc.zrs for ZODB replication. After adding the information to the buildout.cfg, I've added the URL https://pypi.org/simple on the index parameter:
[buildout]
extends =
base.cfg
versions.cfg
index = https://pypi.org/simple
Then I run the buildout and get the following error:
# sudo -u plone_buildout bin/buildout
Installing 'plone.recipe.zeoserver[zrs]'.
We have the distribution that satisfies 'plone.recipe.zeoserver[zrs]==1.2.9'.
Getting required 'zc.zrs'
We have no distributions for zc.zrs that satisfies 'zc.zrs'.
Download error on https://pypi.org/simple: hostname 'pypi.org' doesn't match either of 'www.python.org', '*.python.org', 'docs.python.org', 'downloads.python.org', 'pypi.python.org' -- Some packages may not be found!
Download error on https://pypi.org/simple/zc.zrs/: hostname 'pypi.org' doesn't match either of 'www.python.org', '*.python.org', 'docs.python.org', 'downloads.python.org', 'pypi.python.org' -- Some packages may not be found!
Couldn't find index page for 'zc.zrs' (maybe misspelled?)
Download error on https://pypi.org/simple/: hostname 'pypi.org' doesn't match either of 'www.python.org', '*.python.org', 'docs.python.org', 'downloads.python.org', 'pypi.python.org' -- Some packages may not be found!
Getting distribution for 'zc.zrs'.
Couldn't find index page for 'zc.zrs' (maybe misspelled?)
Could't load zc.buildout entry point default
from plone.recipe.zeoserver[zrs]:
Couldn't find a distribution for 'zc.zrs'..
While:
Installing.
Getting section zeoserver.
Initializing section zeoserver.
Installing recipe plone.recipe.zeoserver[zrs].
Getting distribution for 'zc.zrs'.
Error: Couldn't find a distribution for 'zc.zrs'.
After doing some research find out that the buildout uses easy_install, and tryed to add some parameters described from this documentation, but I'm getting the same errors like doesn't changed nothing.
How can I allow the download from PyPI from Plone buildout?
The Plone buildout should be able to download from pypi by default.
Check if you can download with wget into your download folder:
wget https://files.pythonhosted.org/packages/5c/b2/5a516f4883fc766ea37a9d979a5cacddc1b29df17140c14da26676a3c4b5/zc.zrs-3.1.0.tar.gz
You should have a downloads folder in your buildout-cache folder, if you are using the default installer.
I do that sometimes when the server has some strange network configurations and can't download some packages directly.
I need execute Data Fusion pipelines from Composer, using de operatos for this:
from airflow.providers.google.cloud.operators.datafusion import (
CloudDataFusionCreateInstanceOperator,
CloudDataFusionCreatePipelineOperator,
CloudDataFusionDeleteInstanceOperator,
CloudDataFusionDeletePipelineOperator,
CloudDataFusionGetInstanceOperator,
CloudDataFusionListPipelinesOperator,
CloudDataFusionRestartInstanceOperator,
CloudDataFusionStartPipelineOperator,
CloudDataFusionStopPipelineOperator,
CloudDataFusionUpdateInstanceOperator,
)
The issue I have is about modulo "apache-airflow-backport-providers-google", with the support of this links i knew what I need to use this modulo:
reference to install the modulo in airflow instance (answered by #Gonzalo Pérez Fernández): https://airflow.apache.org/docs/apache-airflow-providers-google/stable/operators/cloud/datafusion.html
when i tried to install python dependency on Composer like PyPi Package i get this error:
UPDATE operation on this environment failed 7 minutes ago with the following error message:
Failed to install PyPI packages.
apache-airflow-providers-google 5.0.0 has requirement google-ads>=12.0.0, but you have google-ads 7.0.0. Check the Cloud Build log at https://console.cloud.google.com/cloud-build/builds/a2ecf37a-4c47-4770-9489-6fb65e87d82f?project=341768372632 for details. For detailed instructions see https://cloud.google.com/composer/docs/troubleshooting-package-installation
the log deail is:
apache-airflow-providers-google 5.0.0 has requirement google-ads>=12.0.0, but you have google-ads 7.0.0.
apache-airflow-backport-providers-google 2021.3.3 has requirement apache-airflow~=1.10, but you have apache-airflow 2.1.2+composer.
The command '/bin/sh -c bash installer.sh $COMPOSER_PYTHON_VERSION fail' returned a non-zero code: 1
ERROR
ERROR: build step 0 "gcr.io/cloud-builders/docker" failed: step exited with non-zero status: 1
is there any way to use de module "apache-airflow-backport-providers-google" without depedency issues on composer instance?, or What would be the best way to use data fusion operators no need to change or parse package versions in python?.
Composer Image version used:
composer-1.17.0-airflow-2.1.2
Thanks.
There is no need to install apache-airflow-backport-providers-google in Airflow 2.0+. This package actually backports Airflow 2 operators into Airflow 1.10.*. In addition, in Composer version composer-1.17.0-airflow-2.1.2 the apache-airflow-providers-google==5.0.0 package is already installed according to the documentation. You should be able to import the Data Fusion operators with the code snippet you posted as is.
However, if this is not the case, you should probably handle the conflict shown in the logs when trying to reinstall apache-airflow-providers-google==5.0.0:
apache-airflow-providers-google 5.0.0 has requirement google-ads>=12.0.0, but you have google-ads 7.0.0.
You can add the requirement for google-ads=12.0.0 in your PyPi dependencies and see if it works.
I am new to Julia's package manager, and I am having trouble installing GLPK and LinProgGLPK.
I have already run Pkg.Init() and have successfully installed Curl using Pkg.add("Curl"). However, when I try to install GLPK or LinProgGLPK (using Pkg.add("GLPK") and Pkg.add("LinProgGLPK")), I get the following message:
MESSAGE: Installing BinDeps v0.0.0
ERROR: Path BinDeps already exists! Please remove to allow installation.
in _resolve at pkg.jl:345
in anonymous at no file:163
in cd at file.jl:26
in cd_pkgdir at pkg.jl:42
in add at pkg.jl:143
in add at pkg.jl:175
I seem to get the same message for other packages that are dependent on BinDeps (including Winston).
I have tried calling Pkg.rm("BinDeps"), Pkg.add("BinDeps"), Pkg.update(), and Pkg.resolve(), and then returned to trying to add GLPK, but the same message persists. I have also entered ~/.julia to remove the BinDeps folder, but that did not work either. What am I missing?
P.S. I am running julia in Linux Ubuntu.
Honestly, when something gets screwed up, it's best just to wipe ~/.julia and re-add the packages.
Just make sure you back up your local changes!