Skip to content

add patch for Tombo 1.5.1 to fix bug with rpy2 v3 when creating DataFrames#11892

Merged
smoors merged 1 commit intoeasybuilders:developfrom
branfosj:20201216150008_new_pr_Tombo151
Dec 16, 2020
Merged

add patch for Tombo 1.5.1 to fix bug with rpy2 v3 when creating DataFrames#11892
smoors merged 1 commit intoeasybuilders:developfrom
branfosj:20201216150008_new_pr_Tombo151

Conversation

@branfosj
Copy link
Copy Markdown
Member

(created using eb --new-pr)

@branfosj
Copy link
Copy Markdown
Member Author

With module load rpy2/3.2.6-foss-2019b-Python-3.7.4:

$ python
Python 3.7.4 (default, Nov 20 2019, 14:37:06)
[GCC 8.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from rpy2 import robjects as r
>>> _R_DF = r.DataFrame(())
Traceback (most recent call last):
  File "/rds/bear-apps/2019b/EL7-haswell/software/rpy2/3.2.6-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/rpy2/robjects/vectors.py", line 1204, in __init__
    kv = [(str(k), conversion.py2rpy(v)) for k, v in obj.items()]
AttributeError: 'tuple' object has no attribute 'items'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/rds/bear-apps/2019b/EL7-haswell/software/rpy2/3.2.6-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/rpy2/robjects/vectors.py", line 1207, in __init__
    'obj can only be'
ValueError: obj can only bean instance of rpy2.rinterface.ListSexpVector, an instance of TaggedList, or an objects with a methods items() that returns (key, value) pairs (such a Python dict, rpy2.rlike.container OrdDict).
>>> _R_DF = r.DataFrame({})

@branfosj
Copy link
Copy Markdown
Member Author

Test report by @branfosj
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0211u03a.bear.cluster - Linux centos linux 7.8.2003, x86_64, Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz (cascadelake), Python 3.6.8
See https://gist.github.com/eaff0972316e4fd4adfa66a9fa40cfea for a full test report.

@branfosj
Copy link
Copy Markdown
Member Author

Test report by @branfosj
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0211u38b.bear.cluster - Linux centos linux 8.2.2004, x86_64, Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz (cascadelake), Python 3.6.8
See https://gist.github.com/1d0558772c5ed68b015f96d10aef7237 for a full test report.

@smoors
Copy link
Copy Markdown
Contributor

smoors commented Dec 16, 2020

Test report by @smoors
SUCCESS
Build succeeded for 2 out of 2 (1 easyconfigs in total)
node376.hydra.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz (skylake_avx512), Python 2.7.5
See https://gist.github.com/4ca15b54868d62f41efe9c64fd7e4ec0 for a full test report.

@smoors
Copy link
Copy Markdown
Contributor

smoors commented Dec 16, 2020

@boegelbot please test @ generoso

@boegelbot
Copy link
Copy Markdown
Collaborator

@smoors: Request for testing this PR well received on generoso

PR test command 'EB_PR=11892 EB_ARGS= /apps/slurm/default/bin/sbatch --job-name test_PR_11892 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 12310

Test results coming soon (I hope)...

Details

- notification for comment with ID 746930195 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

@boegelbot
Copy link
Copy Markdown
Collaborator

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
generoso-c1-s-1 - Linux centos linux 8.2.2004, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/117f5452a95560bea74bee7fe0d72cba for a full test report.

@boegel
Copy link
Copy Markdown
Member

boegel commented Dec 16, 2020

@branfosj Don't hesitate to tag bug fix PRs for the "next release" milestone, so we don't overlook them for the next EasyBuild release...

@smoors smoors added this to the next release (4.3.3?) milestone Dec 16, 2020
Copy link
Copy Markdown
Contributor

@smoors smoors left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

lgtm

@smoors
Copy link
Copy Markdown
Contributor

smoors commented Dec 16, 2020

Going in, thanks @branfosj!

@smoors smoors merged commit 9a30057 into easybuilders:develop Dec 16, 2020
@boegel boegel changed the title Fix Tombo to work with rpy2 v3 when creating DataFrames add patch for Tombo 1.5.1 to fix bug with rpy2 v3 when creating DataFrames Dec 16, 2020
@branfosj branfosj deleted the 20201216150008_new_pr_Tombo151 branch December 16, 2020 20:12
@boegel
Copy link
Copy Markdown
Member

boegel commented Dec 16, 2020

Test report by @boegel
SUCCESS
Build succeeded for 3 out of 3 (1 easyconfigs in total)
node3575.doduo.os - Linux RHEL 8.2, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/7eab3bba0518943986d0feffa1ba79fd for a full test report.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

Projects

None yet

Development

Successfully merging this pull request may close these issues.

4 participants