I must correct some errors in my package antaresProcessing.
I want to reproduce these errors before.
Here, you can see CRAN Checks
I don't have debian OS.
I tried rhub, you can see that the results are ok
I tried to execute these functions, all are fine.
rhub::check_for_cran(platform = 'debian-gcc-devel')
rhub::check_for_cran(platform = 'debian-gcc-patched')
rhub::check_for_cran(platform = 'debian-gcc-release')
Related
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've been using pkgdown::deploy_to_branch() for awhile now to publish my docs on the gh-pages branch of my repo, but as of this week it stopped working and has started giving me the following error:
Error: callr subprocess failed: server certificate verification failed. CAfile: /etc/ssl/certs/ca-certificates.crt CRLfile: none
Type .Last.error.trace to see where the error occurred
7.
stop(cond) at errors.R#275
6.
throw(newerr, parent = remerr[[2]]) at result.R#70
5.
get_result(output = out, options) at eval.R#176
4.
callr::r(function(..., crayon_enabled, crayon_colors, pkgdown_internet) {
options(crayon.enabled = crayon_enabled, crayon.colors = crayon_colors,
pkgdown.internet = pkgdown_internet)
pkgdown::build_site(...) ... at build.r#432
3.
build_site_external(pkg = pkg, examples = examples, run_dont_run = run_dont_run,
seed = seed, lazy = lazy, override = override, preview = preview,
devel = devel) at build.r#385
2.
build_site(pkg, devel = FALSE, preview = FALSE, install = FALSE,
...) at deploy-site.R#172
1.
pkgdown::deploy_to_branch()
When I tried to debug and got deeper into the function, this is the error I got trying to call build_site() directly:
Admittedly, authentication of all sorts is consistently baffling to me, but what has me really baffled is that my auth with github seems to be working in all other ways. I have it cloned with SSH. I can push and pull to my heart's content when I do it manually or through the RStudio GUI. Also, I can't figure out anything that has changed since the time when this was working.
Anyway, any help is much appreciated. I've also looked at a few other issues that came up when I googled the error (this one, for example) but none of them seem to be relevant to my situation where git is working fine except in this call.
Some details:
I'm on Ubuntu 18.04.5 LTS (GNU/Linux 5.4.0-1054-aws x86_64)
R 4.0.3
pkgdown 1.6.1
I tried this with two different repos (1 and 2, both of which were previously working with this same command and the same OS/versions/etc ^
Let me know if there are any more details that would help. Thanks!
Well, it turns out this had nothing to do with pkgdown. Sorry for blaming you pkgdown!
The issue had something to do with this which I was lucky enough to stumble onto the exact day that it happened. A coworker told me to run the following snippet and it fixed everything.
sudo apt-get update ; sudo apt-get install -y ca-certificates
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.
I've spent the last 4 hours trying to find out why I wasn't able to install any packages in R (it started with me trying to install a package I was developing). It would just stall for +5 minutes without doing anything or outputting anything to the terminal. I tracked the issue down to the following call:
repos <- structure("https://cran.rstudio.com/", .Names = "CRAN")
type <- "both"
utils::available.packages(utils::contrib.url(repos, type), type = type)
I realized after a while that it was just the RStudio CRAN mirror, and when I changed the repo to "https://cran.case.edu/", it started working. However, there was literally no indication of this on the surface--and it took forever for me to find out what the problem was.
My question is this: Is there a way of using multiple CRAN repos so when one fails, others are used? Or at least a way that will prevent this from happening again?
I updated my Mac to OS10 and attempting to run RStudio Knit, and get the error:
"evaluate 0.7.2 is required but 0.7 is available".
I tried this and did not fixed the issue:
remove.packages("evaluate")
install.packages("evaluate")
Any help would be appreciated.
Try setting up the below option and by rerunning the code.
getOption("repos")
options(repos = c(CRAN = "https://cran.rstudio.org"))
It also happened to me. I downloaded evaluate zip file from here https://cran.rstudio.com/web/packages/evaluate/index.html
and then manually installed it in R Studio (Tools-InstallPackages-zip file).
Good luck !
install.packages('evaluate')
Warning in install.packages :
unable to access index for repository HTTP://cran.rstudio.com/bin/windows/contrib/3.4:
cannot open URL 'HTTP://cran.rstudio.com/bin/windows/contrib/3.4/PACKAGES'
When you compile the update or remove sentences, if the output like this, you could make some settings, since maybe the problem is your internet. Follow the steps:
Open Rstudio.
Click tools.
Choose global options->packages.
Modify CRAN to the country you living. like, China or Japan. Cause your browser maybe work only you do this.