r-base v4.2.0

[regro-cf-autotick-bot]

It is very likely that the current package version for this feedstock is out of date.

Checklist before merging this PR:

• Dependencies have been updated if changed: see upstream
• Tests have passed
• Updated license if changed and license_file is packaged

Information about this PR:

1. Feel free to push to the bot's branch to update this PR if needed.
2. The bot will almost always only open one PR per version.
3. The bot will stop issuing PRs if more than 3 version bump PRs generated by the bot are open. If you don't want to package a particular version please close the PR.
4. If you want these PRs to be merged automatically, make an issue with @conda-forge-admin,please add bot automerge in the title and merge the resulting PR. This command will add our bot automerge feature to your feedstock.
5. If this PR was opened in error or needs to be updated please add the bot-rerun label to this PR. The bot will close this PR and schedule another one. If you do not have permissions to add this label, you can use the phrase @conda-forge-admin, please rerun bot in a PR comment to have the conda-forge-admin add it for you.

Pending Dependency Version Updates

Here is a list of all the pending dependency version updates for this repo. Please double check all dependencies before merging.

Name	Upstream Version	Current Version
clang-compiler-activation	14.0.1
icu	2022-03-31
libjpeg-turbo	9d
openjdk	11.0.11+9
r-base	4.2.0

Dependency Analysis

We couldn't run dependency analysis due to an internal error in the bot. :( Help is very welcome!

_{This PR was created by the regro-cf-autotick-bot. The regro-cf-autotick-bot is a service to automatically track the dependency graph, migrate packages, and propose package version updates for conda-forge. Feel free to drop us a line if there are any issues! This PR was generated by https://github.com/regro/autotick-bot/actions/runs/2207946089, please use this URL for debugging.}

[conda-forge-linter]

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipe) and found it was in an excellent condition.

[isuruf]

@dpryan79, windows build needs a UCRT build of the toolchain. See conda-forge/conda-forge.github.io#1654

[dpryan79]

Ah, thanks for the heads up @isuruf, I won't bother further with the windows builds for the moment then.

[dpryan79]

Maybe someone with access to PPC64 or ARM can check what library isn't getting linked correctly there.

[dpryan79]

@nturaga As mentioned on gitter

[nturaga]

@nturaga As mentioned on gitter

Thanks @dpryan79

[mjsteinbaugh]

Anything I can do to help resolve this issue? Happy to devote some time later this week.

[dpryan79]

Is anyone able to debug the aarch64 and ppc64le failures?

[mjsteinbaugh]

Seems like they're both hitting the same error:

installing 'sysdata.rda'
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/conda/feedstock_root/build_artifacts/r-base-split_1650831579216/work/library/utils/libs/utils.so':
  /home/conda/feedstock_root/build_artifacts/r-base-split_1650831579216/work/library/utils/libs/utils.so: cannot open shared object file: No such file or directory
Calls: <Anonymous> ... envtable -> loadNamespace -> library.dynam -> dyn.load
Execution halted

I'll see if I can spin up an EC2 instance and try to install R 4.2.0 on ARM

[isuruf]

@conda-forge-admin, rerender

[mjsteinbaugh]

@isuruf Looks like a download step for the Windows build timed out:

+ curl --insecure -C - -o /c/Users/VssAdministrator/Downloads/miktex-portable-2.9.6942.exe -SL https://web.archive.org/web/20190325114245/https://mirrors.rit.edu/CTAN/systems/win32/miktex/setup/windows-x86/miktex-portable-2.9.6942.exe
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  3  180M    3 5741k    0     0  47128      0  1:07:01  0:02:04  1:04:57     0
[...]
  3  180M    3 6525k    0     0  49823      0  1:03:23  0:02:14  1:01:09  179k
curl: (18) transfer closed with 182820312 bytes remaining to read
+ true
+ echo 'Extracting miktex-portable-2.9.6942.exe, this will take some time ...'
+ 7za x -y /c/Users/VssAdministrator/Downloads/miktex-portable-2.9.6942.exe
Extracting miktex-portable-2.9.6942.exe, this will take some time ...
+ exit 1
Traceback (most recent call last):
  File "C:\Miniconda\Scripts\conda-mambabuild-script.py", line 9, in <module>
    sys.exit(main())

[dpryan79]

@conda-forge-admin please rerender

The most recent build issue (just hit rerun) suggests a CI setup issue on windows.

[github-actions]

Hi! This is the friendly automated conda-forge-webservice.

I tried to rerender for you, but it looks like there was nothing to do.

This message was generated by GitHub actions workflow run https://github.com/conda-forge/r-base-feedstock/actions/runs/2413901918.

[dpryan79]

The error on windows is now:

gcc.exe: error: ../../../Library/mingw-w64/lib/sicudt.a: No such file or directory

Should the static library be present in the windows ICU package?

[notestaff]

If the Windows build is taking a while to fix, could just the Linux and OSX builds be updated on conda-forge for now? (By putting old recipe lines under [win] tags and adding the new recipe lines under [unix] tags).

[ZheFrench]

Hi, I'm not sure to understand everything here but integration progress is stuck because of windows stuffs but, Is there finally a way to install 4.2 only for Linux via conda ? Is there any solution that would be provide in a close future , at least for linux, is this possible ?

Forgot what I said, it works now. Tks

conda install -c conda-forge r-base=4.2

[mjsteinbaugh]

@ZheFrench 4.2.0 isn't on conda-forge yet, so that shouldn't work -- that's the point of this pull request

[jdblischak]

Forgot what I said, it works now. Tks

@ZheFrench You likely pulled r-base 4.2.0 from the r/defaults channel. Mixing conda-forge and defaults can quickly lead to problems with your conda environments.

https://anaconda.org/r/r-base/files?version=4.2.0

If you're mainly doing bioinformatics tasks in Linux, I recommend you explicitly ignore the defaults channel by specifying your preferred channels in a user-level .condarc:

conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

This essentially states: "always download from conda-forge unless the package is completely missing, in which case search bioconda". After running the above commands, your .condarc should look like the following:

$ cat ~/.condarc
channels:
  - conda-forge
  - bioconda
channel_priority: strict

[jdblischak]

In case it could be useful, I have built R 4.2.0 for linux-64 and osx-64 using the updated recipe in this PR and then uploaded them to my personal channel.

https://anaconda.org/jdblischak/r-base/files?version=4.2.0

You can install R 4.2.0 with:

mamba create -n r420 -c jdblischak -c conda-forge r-base=4.2.0

Note that while this will install a conda-forge-compatible r-base into your conda env, it's quite limited since the rest of the conda-forge ecoystem hasn't built the conda R packages for R 4.2.0 yet. In other words, you'll need to install the source packages from CRAN instead of the binaries from anaconda.org

Here's how I created these packages:

git clone git@github.com:conda-forge/r-base-feedstock.git
cd r-base-feedstock
git remote add bot git@github.com:regro-cf-autotick-bot/r-base-feedstock.git
git fetch bot
git checkout bot/4.2.0_h34c46c

# osx
conda build recipe/ -m .ci_support/osx_64_.yaml
# linux
conda build recipe/ -m .ci_support/linux_64_.yaml

# test
mamba create -n r420 --use-local r-base=4.2.0
conda activate r420
Rscript --version
conda deactivate

[dpryan79]

Maybe we just disable windows for now and start the migration?

[dpryan79]

@conda-forge/r-base Since this has been stuck for 3 months I propose we skip windows for now and continue on. If no one objects in the next week I'll go ahead and do that.

[conda-forge-linter]

Hi! This is the friendly automated conda-forge-linting service.

I wanted to let you know that I linted all conda-recipes in your PR (recipe) and found some lint.

Here's what I've got...

For recipe:

• The build section contained an unexpected subsection name. slip is not a valid subsection name.

[conda-forge-linter]

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipe) and found it was in an excellent condition.

[dpryan79]

@conda-forge-admin please rerender

[cbrueffer]

👍 from me

[l2dy]

Would other R packages like r-tidyverse automatically get pull requests from conda-forge bots for the 4.2 update?

[dpryan79]

Only once the migration begins

[abalter]

Windows seems to have been entirely left behind. Linux is now at 4.3+, which is great.

Is there any plan to debug Windows compilation?