I installed the latest version of Virtuoso using yum on CentOs. I was able to successfully do that first time. However,when I restarted the virtuoso server after uploading a dataset/CSV file, I am not seeing the 'conductor tab' in the webUI.
I thought something went wrong - and tried to do a clean install. But I have somehow managed to loose conductor completely this time. Below is the log snippet of virtuoso-t.
10:41:00 INFO: PL LOG: Installing Virtuoso Conductor version 1.00.8727 (DAV)
10:41:00 INFO: Checkpoint started
10:41:00 INFO: Checkpoint finished, log reused
10:41:00 INFO: PL LOG: VAD_INSTALL: Please update server version (FATAL)
10:41:00 INFO: PL LOG: Errors where detected during installation of "Virtuoso Conductor".
You report you "installed the latest version of Virtuoso using yum" -- but what version did you actually get? We provide a CentOS-specific guide which may now be outdated if someone has produced a yum package -- but that package may also be outdated.
Please check the version you have actually installed (output of virtuoso-t -? gives the best version string), and be sure it is at least 6.1.8 (if Virtuoso v6) or 7.2.2 (if Virtuoso v7). If not, I would suggest a clean rebuild/reinstall, following our instructions, based on the latest source from GitHub.
For future, questions specifically regarding Virtuoso are often best raised on the public Virtuoso Users mailing list, the public OpenLink Support Forums, or through a confidential Support Case. ObDisclaimer: I work for OpenLink Software, producer of Virtuoso.
Related
I want to set up rstudio-server on an iMac with support for multiple users and remote login. I followed the steps in the INSTALL tutorial: I built the source, set up the configuration files and the launchd daemon. At first, it works fine, but after some time, I get these warnings/errors when I plot:
2022-06-09 08:02:29.438 rsession[3050:139329] XType: failed to connect - Error Domain=NSCocoaErrorDomain Code=4099 "The connection to service named com.apple.fonts was invalidated: failed at lookup with error 3 - No such process." UserInfo={NSDebugDescription=The connection to service named com.apple.fonts was invalidated: failed at lookup with error 3 - No such process.}
2022-06-09 08:02:29.438 rsession[3050:139329] Font server protocol version mismatch (expected:5 got:0), falling back to local fonts
2022-06-09 08:02:29.438 rsession[3050:139329] XType: unable to make a connection to the font daemon!
2022-06-09 08:02:29.438 rsession[3050:139329] XType: XTFontStaticRegistry is enabled as fontd is not available.
Then I can't plot any more unless I restart R and re-run my code. Do you know what could be the issue? I could not get any help when opening an issue on the rstudio-server github since MacOS is not officially supported.
I was also looking at running rstudio-server via docker, but I couldn't find a good way to map the user namespace from macOS to the container.
Any help or suggestion would be greatly appreciated!
EDIT: It seems I was able to solve the issue by launching the fontd daemon with:
sudo launchctl load -w /System/Library/LaunchAgents/com.apple.fontd.useragent.plist
This seems like an issue with the MacOS font daemon, not with RStudio itself.
Someone reported a similar issue on PhantomJS. Rebooting resolved it for them.
This answer reported the same error for a different build, and they were able to resolve it by installing the correct "Apple Worldwide Developer Relations Certification Authority" in Keychain:
The one I had had an expiration date of February 2023. I deleted that one and went here, downloaded the one called "Worldwide Developer Relations - G3 (Expiring 02/20/2030 00:00:00 UTC)", then retried the build and it worked.
I can not find how to replicate the internal CRAN test for the URLs healthy.
It is important that this test is run only on the Debian winbuilder (yes, debian under winbuilder). As this test is not run on the Windows machine so we could NOT use the https://win-builder.r-project.org/upload.aspx website service to replicate it.
The example error message from the CRAN server, as the website was moved.
Such message is producing the NOTE so the package is not automatically processed.
Found the following (possibly) invalid URLs:
URL: http://blog.obeautifulcode.com/R/How-R-Searches-And-Finds-Stuff/
From: inst/doc/tinyverse.html
Status: Error
Message: Could not resolve host: blog.obeautifulcode.com
Edit:
There is a useful source with CRAN policy in this area https://cran.r-project.org/web/packages/URL_checks.html
(Promoting comment to answer as suggested...)
The test code has been pulled out of R itself and made into a package you can install. Other than that it is of course part of any (recent enough) R or R-devel build.
FWIW I also wrapped this into a convenience script I call all the time on my systems.
I am trying to install the ggpattern package from GitHub (https://www.rdocumentation.org/packages/ggpattern/versions/0.2.0)
I've reinstalled R, followed the all steps according to the site, also tried
remotes::install_github("coolbutuseless/ggpattern", force = TRUE)
But I still get:
Error: Failed to install 'unknown package' from GitHub:
HTTP error 401.
Bad credentials
Rate limit remaining: 19/60
Rate limit reset at: 2022-01-29 18:28:15 UTC
I'm working on R version 4.1.2 (newest according to me) on Windows.
Do you have any idea what is the issue here?
You need to check if you have a personal access token set in your environment. For example, when I have a Git project, I set a personal access token. However, I set this in the project environment, so that it isn't any issues outside of that environment.
To see if there is one assigned:
Sys.getenv("GITHUB_PAT")
If there is one set, write it down (you may need that in the future).
To remove it, so you can install the GitHub package:
Sys.unsetenv("GITHUB_PAT")
Having an issue running airflow on my M1 Mac. Keeps erroring out with error in Flask-OpenID setup command: use_2to3 is invalid. I have setuptools < 58 and still having issues.
ERROR: Could not find a version that satisfies the requirement flask-openid==1.2.5 (from versions: 0.9, 0.9.1, 1.0, 1.0.1, 1.1, 1.1.1, 1.2, 1.2.1, 1.2.2, 1.2.3, 1.2.4, 1.2.5, 1.3.0)
ERROR: No matching distribution found for flask-openid==1.2.5
Yes. It's been fixed in flask_openid 1.2.6 (It's not a problem with Airflow but with FlaskOpenID).
Looks like for some reason your setuptools is not what you think it is. See:
https://github.com/pallets-eco/flask-openid/issues/59
You have not explained a crucial things - how you are installing airflow, neither which version of Airflow you try to install - which does not help in trying to help you unfortunately, so I have to make some guesses. Here is what you can do if you cannot - for any reason - downgrade to setuptools < 0.58.
If you are using Airlfow 2 and using constraints (as you should - this is the only supported way https://airflow.apache.org/docs/apache-airflow/stable/installation/installing-from-pypi.html) for some older version of Airflow, then possibly flask-openid is 1.2.5 in those old constraint versions. Please check it and if you REALLY want to stay with an older version, then you can download the constraint file locally, modify flask-openid version to 1.2.6 and point to the file instead of the github URL as you should do normally (If you don't use constraints - start using them immediately).
However, better option than installing an old version of Airflow, will be to update to the latest version of Airflow (currently 2.2.2 but we are about to start voting on 2.2.3), where this problem is for sure fixed (also in few other versions). Airflow folows SemVer so you should be generally safe to migrate to 2.2.2 if you've used an earlier version of Airflow 2.
If you are trying to install Airflow 1.10.* - then don't do it. Move Airflow 2 immediately. Airflow 1.10 has reached end of life in June 2021 and it's almost half a year as it did not receive any fixes - it won't receive any fixes for the Flask OpenID problem, so you are pretty much on your own here.
Also you make yourself vulnerable to unpatched security issues (Airlfow 1.10 stopped receiving also critical security fixes as of June 2021).
I'm having issues with Azure Machine Learning SDK for R: "module 'azureml' has no attribute 'core'"...
For reasons that aren't my own, I have to use azureml to apply machine learning (my own stuff, written in R) to data from our data warehouse that is put in the blob storage. The modelled output should be put back into the blob storage so it can be accessed from the data warehouse.
I've written the code in R on my local machine (stored in a git repo). Preferably, I'd find some method to pull my code from git into a pipeline in the azureml environment so that it can be directly run whenever new data is available in the blob storage.
I've embarked on a tutorial-spree and found this seemingly relevant walkthrough: Train and deploy your first model with Azure ML (and this one).
But... after trying all I could think of, I'm stuck on the first steps. After installing all (or at least.. that's what I think) packages, modules, apps etc, and running the following code in RStudio:
library(azuremlsdk)
existing_ws <- get_workspace(name = name,
subscription_id = subscription_id,
resource_group)
I run into an error that I haven't been able to fix:
AttributeError: module 'azureml' has no attribute 'core'
It seems that the azuerml is supposed to have an attribute "core", but when looking at it more closely, there is indeed no such attribute.
The function "get_workspace()" is trying to access: "azureml$core$Workspace$get".
I found that "azuerML$Workspace" does exist, but then I can't figure out how to make that work.
Can anyone explain to me why I'm encountering this error?
Does anyone know of a better tutorial on how to connect my R code the azureml's cloud service?
Any pointers in the right direction are much appreciated!
EDITS - still not solved:
After advice from others, I double, triple and quadruple checked the installation.
I updated R and I'm now running:
R.version
platform x86_64-w64-mingw32
arch x86_64
os mingw32
system x86_64, mingw32
status
major 3
minor 6.2
year 2019
month 12
day 12
svn rev 77560
language R
version.string R version 3.6.2 (2019-12-12)
nickname Dark and Stormy Night
I installed Conda with Python 3.6.10.
I installed the azuremlsdk R package (I tried both provided options).
I then realized that there are some inconsistencies with the versions of the azure-modules, so I also tried installing it with the keyword 'multi-arch':
remotes::install_cran('azuremlsdk', repos = 'http://cran.us.r-project.org', INSTALL_opts=c("--no-multiarch"))
Then, I installed the azureml python sdk.
I had a look at all the versions again (using python -m pip freeze):
azure-common==1.1.24
azure-graphrbac==0.61.1
azure-mgmt-authorization==0.60.0
azure-mgmt-containerregistry==2.8.0
azure-mgmt-keyvault==2.0.0
azure-mgmt-resource==7.0.0
azure-mgmt-storage==7.1.0
azureml==0.2.7
azureml-automl-core==1.0.83.1
azureml-core==1.0.69
azureml-dataprep==1.1.36
azureml-dataprep-native==13.2.0
azureml-pipeline==1.0.69
azureml-pipeline-core==1.0.69
azureml-pipeline-steps==1.0.69
azureml-sdk==1.0.69
azureml-telemetry==1.0.69
azureml-train==1.0.69
azureml-train-automl-client==1.0.83
azureml-train-core==1.0.69
azureml-train-restclients-hyperdrive==1.0.69
As I was surprised to see all the 1.0.69 versions, instead of the 1.0.83 versions, I re-installed the azureml python sdk using:
azuremlsdk::install_azureml(version = "1.0.83")
This worked, in the sense that indeed all versions are now 1.0.83:
azure-common==1.1.24
azure-graphrbac==0.61.1
azure-mgmt-authorization==0.60.0
azure-mgmt-containerregistry==2.8.0
azure-mgmt-keyvault==2.0.0
azure-mgmt-resource==7.0.0
azure-mgmt-storage==7.1.0
azureml==0.2.7
azureml-automl-core==1.0.83.1
azureml-core==1.0.83
azureml-dataprep==1.1.36
azureml-dataprep-native==13.2.0
azureml-pipeline==1.0.83
azureml-pipeline-core==1.0.83
azureml-pipeline-steps==1.0.83
azureml-sdk==1.0.83
azureml-telemetry==1.0.83
azureml-train==1.0.83
azureml-train-automl-client==1.0.83
azureml-train-core==1.0.83
azureml-train-restclients-hyperdrive==1.0.83
But still... I get the error with the missing core. I get it both when running:
library(azuremlsdk)
get_current_run()
and also when running:
library(azuremlsdk)
existing_ws <- get_workspace(name = name,
subscription_id = subscription_id,
resource_group)
Note that the first time running this code after starting up RStudio, I get the error:
Error in py_get_attr_impl(x, name, silent) :
AttributeError: module 'azureml' has no attribute '_base_sdk_common'
And every time after that I get this error:
Error in py_get_attr_impl(x, name, silent) :
AttributeError: module 'azureml' has no attribute 'core'
Any help would be much appreciated!
This issue was introduced by the latest reticulate 1.14 release, in which reticulate would create a default r-reticulate conda environment. Since Azure ML was installing the python SDK in an environment named r-azureml, the r-reticulate environment used by reticulate was missing the python SDK. A fix for this issue was addressed in a PR and has been merged into master. Please install from GitHub for now if you have reticulate version 1.14 and are running into this issue. We will be releasing an update to CRAN shortly.
I seemed to have fixed the issue by specifically installing the python package azureml AND azureml.core:
python -m pip install azureml
and then...
python -m pip install azureml.core
I did this for the Conda version that was called by R (r-reticulate). It's a bit odd to not be able to use the Conda environment 'r-azureml' without R switching back to 'r-reticulate', but ah well... at least I don't get my 'azureml' has no attribute 'core' anymore.