Streamline binaries by koppor · Pull Request #15085 · JabRef/jabref

koppor · 2026-02-11T14:12:24Z

In preparation to parallel on GitHub's parallel feature - https://github.com/orgs/community/discussions/14484#discussioncomment-15480826

Make variants in binaries.yml explicit by introducing a composite action.

Switched to environment variables to pass version info - workaround for avelino/jbundle#59
Also creates jabls-cli-6.0-all.jar and jabkit-6.0-all.jar, which can be run using java -jar

gradle vs. gradlew

We CANNOT cache gradlew - see gradle/actions#273 (comment) --> we run with Gradle 9.3.1 and hope that it behaves same as the patched version. On Windows still our patched version is used.

When using setup-gradle in the sub action, gradle is not available...

Steps to test

See workflow running

Checklist

I own the copyright of the code submitted and I license it under the MIT license
[/] I manually tested my changes in running JabRef (always required)
[/] I added JUnit tests for changes (if applicable)
[/] I added screenshots in the PR description (if change is visible to the user)
[/] I added a screenshot in the PR description showing a library with a single entry with me as author and as title the issue number
I described the change in CHANGELOG.md in a way that can be understood by the average user (if change is visible to the user)
[/] I checked the user documentation for up to dateness and submitted a pull request to our user documentation repository

testlens-app · 2026-02-11T14:42:31Z

🚨 TestLens detected 62 failed tests 🚨

Here is what you can do:

Inspect the test failures carefully.
If you are convinced that some of the tests are flaky, you can mute them below.
Finally, trigger a rerun by checking the rerun checkbox.

Test Summary

Check	Project/Task	Test	Runs
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	ArXivFetcherTest > canReplicateArXivOnlySearchByPassingNullParameter()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	ArXivFetcherTest > findFullTextByDOI()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	ArXivFetcherTest > findFullTextByEprint()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	ArXivFetcherTest > findFullTextByEprintWithPrefix()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	ArXivFetcherTest > findFullTextByEprintWithUnknownDOI()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	ArXivFetcherTest > findFullTextByTitle()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	ArXivFetcherTest > findFullTextByTitleAndPartOfAuthor()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	ArXivFetcherTest > findFullTextByTitleWithColonAndJournalWithoutEprint()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	ArXivFetcherTest > findFullTextByTitleWithColonAndUrlWithoutEprint()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	ArXivFetcherTest > findFullTextByTitleWithCurlyBracket()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	ArXivFetcherTest > findFullTextByTitleWithCurlyBracketAndPartOfAuthor()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	ArXivFetcherTest > noSupportsAuthorSearchWithLastFirstName()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	ArXivFetcherTest > retrievePartialResultWhenCannotGetInformationFromArXivAssignedDOI()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	ArXivFetcherTest > retrievePartialResultWhenCannotGetInformationFromUserAssignedDOI()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	ArXivFetcherTest > retrievePureArxivEntryWhenAllDOIFetchingFails()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	ArXivFetcherTest > searchEntryByIdWith4Digits()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	ArXivFetcherTest > searchEntryByIdWith4DigitsAndPrefix()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	ArXivFetcherTest > searchEntryByIdWith4DigitsAndPrefixAndNotTrimmed()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	ArXivFetcherTest > searchEntryByIdWith4DigitsAndVersion()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	ArXivFetcherTest > searchEntryByOldId()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	ArXivFetcherTest > searchEntryByPartOfTitle()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	ArXivFetcherTest > searchEntryByPartOfTitleWithAcuteAccent()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	ArXivFetcherTest > searchWithHttpUrl()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	ArXivFetcherTest > searchWithHttpsUrl()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	ArXivFetcherTest > searchWithHttpsUrlNotTrimmed()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	ArXivFetcherTest > supportsBooleanANDSearch()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	ArXivFetcherTest > supportsPhraseSearch()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	ArXivFetcherTest > supportsPhraseSearchAndMatchesExact()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	CompositeIdFetcherTest > performSearchByIdReturnsCorrectEntryForIdentifier(String, BibEntry, String) > 1 "performSearchByIdReturnsCorrectEntryForArXivId"	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	CrawlerTest > whetherAllFilesAreCreated()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	CrossRefTest > performSearchByIdFindsPaperWithoutTitle()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	GrobidPlainCitationParserTest > grobidPerformSearchCorrectResultTest(String, BibEntry, String) > "example1"	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	GrobidPlainCitationParserTest > grobidPerformSearchCorrectResultTest(String, BibEntry, String) > "example2"	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	GrobidPlainCitationParserTest > grobidPerformSearchCorrectResultTest(String, BibEntry, String) > "example3"	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	GrobidPlainCitationParserTest > grobidPerformSearchCorrectResultTest(String, BibEntry, String) > "example4"	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	GrobidPlainCitationParserTest > grobidPerformSearchWithEmptyStringTest()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	GrobidServiceTest > extractsReferencesFromPdf()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	GrobidServiceTest > processEmptyStringTest()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	GrobidServiceTest > processPdfTest()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	GrobidServiceTest > processValidCitationTest()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	ISIDOREFetcherTest > author()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	ISIDOREFetcherTest > checkThesis()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	ISIDOREFetcherTest > noResults()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	LOBIDIsbnFetcherTest > searchByIdSuccessfulWithLongISBN()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	LOBIDIsbnFetcherTest > searchByIdSuccessfulWithShortISBN()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	LibraryOfCongressTest > performSearchById()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	MedlineFetcherTest > searchByIDSari()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	OpenAlexFetcherTest > getURLForQueryBuildsSearchUrl()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	OpenAlexFetcherTest > getURLForQueryWithLucene()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	OpenAlexFetcherTest > parserParsesResultsArray()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	OpenAlexFetcherTest > parserParsesSingleWorkObject()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	OpenAlexFetcherTest > searchByQueryFindsEntry()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	OpenAlexFetcherTest > searchByQuotedQueryFindsEntry()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	PdfMergeMetadataImporterTest > fetchArxivInformationForPdfWithArxivId()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	PdfMergeMetadataImporterTest > importRelativizesFilePath()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	PdfMergeMetadataImporterTest > pdfMetadataExtractedFrom2024SPLCBecker()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	SemanticScholarCitationFetcherTest > smoke()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	SemanticScholarTest > getDocument()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	URLDownloadTest > test429ErrorThrowsFetcherClientException()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	URLDownloadTest > test503ErrorThrowsFetcherServerException()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	ZbMATHTest > searchByEntryFindsEntry()	❌
Fetcher Tests / Fetcher tests	:jablib:fetcherTest	ZbMATHTest > searchByIdInEntryFindsEntry()	❌

🏷️ Commit: 2961fd7
▶️ Tests: 11600 executed
⚪️ Checks: 65/65 completed

Test Failures (first 5 of 62)

ArXivFetcherTest > canReplicateArXivOnlySearchByPassingNullParameter() (:jablib:fetcherTest in Fetcher Tests / Fetcher tests)

org.opentest4j.AssertionFailedError: expected: <Optional[@article{,
  abstract = {Bacteria tightly regulate and coordinate the various events in their cell cycles to duplicate themselves accurately and to control their cell sizes. Growth of Escherichia coli, in particular, follows a relation known as Schaechter 's growth law. This law says that the average cell volume scales exponentially with growth rate, with a scaling exponent equal to the time from initiation of a round of DNA replication to the cell division at which the corresponding sister chromosomes segregate. Here, we sought to test the robustness of the growth law to systematic perturbations in cell dimensions achieved by varying the expression levels of mreB and ftsZ. We found that decreasing the mreB level resulted in increased cell width, with little change in cell length, whereas decreasing the ftsZ level resulted in increased cell length. Furthermore, the time from replication termination to cell division increased with the perturbed dimension in both cases. Moreover, the growth law remained valid over a range of growth conditions and dimension perturbations. The growth law can be quantitatively interpreted as a consequence of a tight coupling of cell division to replication initiation. Thus, its robustness to perturbations in cell dimensions strongly supports models in which the timing of replication initiation governs that of cell division, and cell volume is the key phenomenological variable governing the timing of replication initiation. These conclusions are discussed in the context of our recently proposed adder-per-origin model, in which cells add a constant volume per origin between initiations and divide a constant time after initiation.},
  author = {Hai Zheng and Po-Yi Ho and Meiling Jiang and Bin Tang and Weirong Liu and Dengjin Li and Xuefeng Yu and Nancy E. Kleckner and Ariel Amir and Chenli Liu},
  date = {2017-01-03},
  doi = {10.1073/pnas.1617932114},
  eprint = {1701.00587},
  eprintclass = {q-bio.CB},
  eprinttype = {arXiv},
  file = {:http\://arxiv.org/pdf/1701.00587v1:PDF},
  journal = {PNAS December 27, 2016 vol. 113 no. 52 15000-15005},
  keywords = {q-bio.CB},
  title = {Interrogating the Escherichia coli cell cycle by cell dimension perturbations},
  _jabref_shared = {sharedId: -1, version: 1}
}]> but was: <Optional[@article{,
  abstract = {Bacteria tightly regulate and coordinate the various events in their cell cycles to duplicate themselves accurately and to control their cell sizes. Growth of Escherichia coli, in particular, follows a relation known as Schaechter 's growth law. This law says that the average cell volume scales exponentially with growth rate, with a scaling exponent equal to the time from initiation of a round of DNA replication to the cell division at which the corresponding sister chromosomes segregate. Here, we sought to test the robustness of the growth law to systematic perturbations in cell dimensions achieved by varying the expression levels of mreB and ftsZ. We found that decreasing the mreB level resulted in increased cell width, with little change in cell length, whereas decreasing the ftsZ level resulted in increased cell length. Furthermore, the time from replication termination to cell division increased with the perturbed dimension in both cases. Moreover, the growth law remained valid over a range of growth conditions and dimension perturbations. The growth law can be quantitatively interpreted as a consequence of a tight coupling of cell division to replication initiation. Thus, its robustness to perturbations in cell dimensions strongly supports models in which the timing of replication initiation governs that of cell division, and cell volume is the key phenomenological variable governing the timing of replication initiation. These conclusions are discussed in the context of our recently proposed adder-per-origin model, in which cells add a constant volume per origin between initiations and divide a constant time after initiation.},
  author = {Hai Zheng and Po-Yi Ho and Meiling Jiang and Bin Tang and Weirong Liu and Dengjin Li and Xuefeng Yu and Nancy E. Kleckner and Ariel Amir and Chenli Liu},
  date = {2017-01-03},
  doi = {10.1073/pnas.1617932114},
  eprint = {1701.00587},
  eprintclass = {q-bio.CB},
  eprinttype = {arXiv},
  file = {:https\://arxiv.org/pdf/1701.00587v1:PDF},
  journal = {PNAS December 27, 2016 vol. 113 no. 52 15000-15005},
  keywords = {q-bio.CB},
  title = {Interrogating the Escherichia coli cell cycle by cell dimension perturbations},
  _jabref_shared = {sharedId: -1, version: 1}
}]>
	at org.junit.jupiter.api.AssertionFailureBuilder.build(AssertionFailureBuilder.java:158)
	at org.junit.jupiter.api.AssertionFailureBuilder.buildAndThrow(AssertionFailureBuilder.java:139)
	at org.junit.jupiter.api.AssertEquals.failNotEqual(AssertEquals.java:201)
	at org.junit.jupiter.api.AssertEquals.assertEquals(AssertEquals.java:184)
	at org.junit.jupiter.api.AssertEquals.assertEquals(AssertEquals.java:179)
	at org.junit.jupiter.api.Assertions.assertEquals(Assertions.java:1188)
	at org.jabref.logic.importer.fetcher.ArXivFetcherTest.canReplicateArXivOnlySearchByPassingNullParameter(ArXivFetcherTest.java:516)

ArXivFetcherTest > findFullTextByDOI() (:jablib:fetcherTest in Fetcher Tests / Fetcher tests)

org.opentest4j.AssertionFailedError: expected: <Optional[http://arxiv.org/pdf/cond-mat/0406246v1]> but was: <Optional[https://arxiv.org/pdf/cond-mat/0406246v1]>
	at org.junit.jupiter.api.AssertionFailureBuilder.build(AssertionFailureBuilder.java:158)
	at org.junit.jupiter.api.AssertionFailureBuilder.buildAndThrow(AssertionFailureBuilder.java:139)
	at org.junit.jupiter.api.AssertEquals.failNotEqual(AssertEquals.java:201)
	at org.junit.jupiter.api.AssertEquals.assertEquals(AssertEquals.java:184)
	at org.junit.jupiter.api.AssertEquals.assertEquals(AssertEquals.java:179)
	at org.junit.jupiter.api.Assertions.assertEquals(Assertions.java:1188)
	at org.jabref.logic.importer.fetcher.ArXivFetcherTest.findFullTextByDOI(ArXivFetcherTest.java:201)

ArXivFetcherTest > findFullTextByEprint() (:jablib:fetcherTest in Fetcher Tests / Fetcher tests)

org.opentest4j.AssertionFailedError: expected: <Optional[http://arxiv.org/pdf/1603.06570v1]> but was: <Optional[https://arxiv.org/pdf/1603.06570v1]>
	at org.junit.jupiter.api.AssertionFailureBuilder.build(AssertionFailureBuilder.java:158)
	at org.junit.jupiter.api.AssertionFailureBuilder.buildAndThrow(AssertionFailureBuilder.java:139)
	at org.junit.jupiter.api.AssertEquals.failNotEqual(AssertEquals.java:201)
	at org.junit.jupiter.api.AssertEquals.assertEquals(AssertEquals.java:184)
	at org.junit.jupiter.api.AssertEquals.assertEquals(AssertEquals.java:179)
	at org.junit.jupiter.api.Assertions.assertEquals(Assertions.java:1188)
	at org.jabref.logic.importer.fetcher.ArXivFetcherTest.findFullTextByEprint(ArXivFetcherTest.java:207)

ArXivFetcherTest > findFullTextByEprintWithPrefix() (:jablib:fetcherTest in Fetcher Tests / Fetcher tests)

org.opentest4j.AssertionFailedError: expected: <Optional[http://arxiv.org/pdf/1603.06570v1]> but was: <Optional[https://arxiv.org/pdf/1603.06570v1]>
	at org.junit.jupiter.api.AssertionFailureBuilder.build(AssertionFailureBuilder.java:158)
	at org.junit.jupiter.api.AssertionFailureBuilder.buildAndThrow(AssertionFailureBuilder.java:139)
	at org.junit.jupiter.api.AssertEquals.failNotEqual(AssertEquals.java:201)
	at org.junit.jupiter.api.AssertEquals.assertEquals(AssertEquals.java:184)
	at org.junit.jupiter.api.AssertEquals.assertEquals(AssertEquals.java:179)
	at org.junit.jupiter.api.Assertions.assertEquals(Assertions.java:1188)
	at org.jabref.logic.importer.fetcher.ArXivFetcherTest.findFullTextByEprintWithPrefix(ArXivFetcherTest.java:213)

ArXivFetcherTest > findFullTextByEprintWithUnknownDOI() (:jablib:fetcherTest in Fetcher Tests / Fetcher tests)

org.opentest4j.AssertionFailedError: expected: <Optional[http://arxiv.org/pdf/1603.06570v1]> but was: <Optional[https://arxiv.org/pdf/1603.06570v1]>
	at org.junit.jupiter.api.AssertionFailureBuilder.build(AssertionFailureBuilder.java:158)
	at org.junit.jupiter.api.AssertionFailureBuilder.buildAndThrow(AssertionFailureBuilder.java:139)
	at org.junit.jupiter.api.AssertEquals.failNotEqual(AssertEquals.java:201)
	at org.junit.jupiter.api.AssertEquals.assertEquals(AssertEquals.java:184)
	at org.junit.jupiter.api.AssertEquals.assertEquals(AssertEquals.java:179)
	at org.junit.jupiter.api.Assertions.assertEquals(Assertions.java:1188)
	at org.jabref.logic.importer.fetcher.ArXivFetcherTest.findFullTextByEprintWithUnknownDOI(ArXivFetcherTest.java:221)

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koppor · 2026-02-12T15:34:56Z

(demo)

github-actions · 2026-02-13T08:38:54Z

The build of this PR is available at https://builds.jabref.org/pull-15085/.

* upstream/main: Refine Automatic Field Editor filtering logic (fixes JabRef#15066) (JabRef#15094) Output URL to workflow Fix token Refine stats message Quick fix to reduce load on runners "Debug" output for assign-issue-action Streamline pr-comment.yml (and remove status: stale label) Feature provide insights citation fetcher (JabRef#15093) Automatic Grouping By Entry Type (JabRef#15081) Minor test fixes for arXiv (JabRef#15100) New Crowdin updates (JabRef#15101) recomment linked files handler (JabRef#15105) Chore(deps): Bump jablib/src/main/resources/csl-styles (JabRef#15087) Streamline binaries (JabRef#15085)

koppor added 2 commits February 11, 2026 15:01

Introduce actions/package

e6790d3

Re-order

1bd0397

koppor added the dev: ci-cd label Feb 11, 2026

koppor added 3 commits February 11, 2026 15:17

jablib jar is requried

499c506

Fix headings

be3a3af

Fix --help at JabSrv

34112c1

koppor added 8 commits February 11, 2026 16:35

Upload directly after successful biuld

f3e1eb4

Prepare use of upcoming GitHub parallel feature

6df5548

Add missing parameters

948a1b2

Have "jabsrv" in the help (instead of "server")

8ebc2d8

Refine future workflow

e4368c7

Fix indnet

952dd37

Add forgotten if

1eb0688

Try to upload distribution files only

086aeaf

koppor added the dev: binaries Binary builds should be uploaded to builds.jabref.org label Feb 11, 2026

koppor added 14 commits February 11, 2026 18:06

Merge branch 'main' into add-actions-package

6a63bd1

Fix target

1365039

Also fail on rsync errors

1c98714

Fix path

78ed329

Try to fix upload

1964b73

Fix paths

08a96e6

Fix cmd rsync

fb2f0f6

Fix dir

de9e705

Remove non-required files

e5655be

Delete on Linux only

550d0f8

Some more waits here and there

5f37dd5

Remove -100-jar

94c018a

Remove eaJdkBuild

48fa5dc

Switch to environment variables VERSION and VERSION_INFO

0e333cf

koppor added 11 commits February 12, 2026 12:00

Route URL through

e854c31

Reoder

62326ba

Fix directory of back link

34e994c

Fix path at target check

40025a9

Use "gradle" instead of patched version

252986a

Setup current gradle version

be1996e

Different gradle on Linux and Windows

3aafc59

Fix API keys

7dc3ce7

Fix fetcher tests running

09dc11e

Fix conditions for fetcher tests

18c95c7

Fix message

7e96182

koppor enabled auto-merge February 12, 2026 15:47

koppor added the automerge PR is tagged with that label will be merged if workflows are green label Feb 12, 2026

jabref-machine approved these changes Feb 12, 2026

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koppor removed the automerge PR is tagged with that label will be merged if workflows are green label Feb 12, 2026

koppor added this pull request to the merge queue Feb 12, 2026

github-actions bot added the status: to-be-merged PRs which are accepted and should go into the merge-queue. label Feb 12, 2026

github-merge-queue bot removed this pull request from the merge queue due to failed status checks Feb 12, 2026

Merge branch 'main' into add-actions-package

2961fd7

koppor added the automerge PR is tagged with that label will be merged if workflows are green label Feb 13, 2026

jabref-machine approved these changes Feb 13, 2026

View reviewed changes

koppor enabled auto-merge February 13, 2026 07:56

jabref-machine approved these changes Feb 13, 2026

View reviewed changes

koppor added this pull request to the merge queue Feb 13, 2026

Merged via the queue into main with commit 30f4537 Feb 13, 2026
59 of 66 checks passed

koppor deleted the add-actions-package branch February 13, 2026 08:59

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Streamline binaries#15085

Streamline binaries#15085
koppor merged 48 commits intomainfrom
add-actions-package

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🚨 TestLens detected 62 failed tests 🚨

Test Summary

Test Failures (first 5 of 62)

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