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Installation issues for version 4.3.1 #5258

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sebastian-brunner opened this issue Aug 29, 2019 · 1 comment
Closed

Installation issues for version 4.3.1 #5258

sebastian-brunner opened this issue Aug 29, 2019 · 1 comment

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@sebastian-brunner
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I try to use the newest Jabref version, as I get these freezes you reported at (http://help.jabref.org/en/Installation#freezes-when-running-jabref). However, I am continuously getting the following error:

Error: Could not find or load main class org.jabref.JabRefMain
Caused by: java.lang.NoClassDefFoundError: javafx/application/Application

I use Ubuntu 18.04 and try with Jabref version 4.3.1 from https://www.fosshub.com/JabRef.html

So far I tried:

Your install instructions: http://help.jabref.org/en/Installation#jabref-4x-1
They fail at line: Install: sudo apt-get install oracle-java8-installer

You claim at https://github.com/JabRef/jabref#installation that jabref is supporting Java 11 or higher, however in your installation instructions (http://help.jabref.org/en/Installation#jabref-4x-1) you say it does not support java 11.

Nevertheless, I tried java 11 using the default-jdk package including openjfx which was reported to work: http://discourse.jabref.org/t/jabref-4-3-1-with-debian-stable/1197 => no luck, see error above

As you claim supporting 11 or higher I installed oracle java 12 as well (similar to https://tecadmin.net/install-oracle-java-11-ubuntu-18-04-bionic/) => see error above

Then I went back to good old java 8 (openjdk) using your install instructions for openjfx from http://help.jabref.org/en/Installation#jabref-4x-1

The version launches, however I get weird behavior using the search field in the top bar (the cursor does not move, when using the arrow keys) and I get the stacktrace appended at the end of the issue.

For now I switch back to the Jabref version from the Ubuntu packages by using sudo apt-get install jabref

Stacktrace:

File: grouptree.fxml not found, attempting with camel case
File: grouptree.css not found, attempting with camel case
java.lang.NullPointerException
	at com.sun.javafx.sg.prism.NGText.renderText(NGText.java:297)
	at com.sun.javafx.sg.prism.NGText.renderContent2D(NGText.java:270)
	at com.sun.javafx.sg.prism.NGShape.renderContent(NGShape.java:261)
	at com.sun.javafx.sg.prism.NGNode.doRender(NGNode.java:2053)
	at com.sun.javafx.sg.prism.NGNode.render(NGNode.java:1945)
	at com.sun.javafx.sg.prism.NGGroup.renderContent(NGGroup.java:235)
	at com.sun.javafx.sg.prism.NGRegion.renderContent(NGRegion.java:577)
	at com.sun.javafx.sg.prism.NGNode.renderForClip(NGNode.java:2294)
	at com.sun.javafx.sg.prism.NGNode.renderRectClip(NGNode.java:2188)
	at com.sun.javafx.sg.prism.NGNode.renderClip(NGNode.java:2214)
	at com.sun.javafx.sg.prism.NGNode.doRender(NGNode.java:2047)
	at com.sun.javafx.sg.prism.NGNode.render(NGNode.java:1945)
	at com.sun.javafx.sg.prism.NGGroup.renderContent(NGGroup.java:235)
	at com.sun.javafx.sg.prism.NGRegion.renderContent(NGRegion.java:577)
	at com.sun.javafx.sg.prism.NGNode.doRender(NGNode.java:2053)
	at com.sun.javafx.sg.prism.NGNode.render(NGNode.java:1945)
	at com.sun.javafx.tk.quantum.ViewPainter.doPaint(ViewPainter.java:477)
	at com.sun.javafx.tk.quantum.ViewPainter.paintImpl(ViewPainter.java:323)
	at com.sun.javafx.tk.quantum.UploadingPainter.run(UploadingPainter.java:134)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
	at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:308)
	at com.sun.javafx.tk.RenderJob.run(RenderJob.java:58)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at com.sun.javafx.tk.quantum.QuantumRenderer$PipelineRunnable.run(QuantumRenderer.java:125)
	at java.lang.Thread.run(Thread.java:748)
10:21:32.777 [AWT-EventQueue-1] ERROR org.jabref.FallbackExceptionHandler - Uncaught exception occurred in Thread[AWT-EventQueue-1,6,main]
java.lang.NullPointerException: null
	at com.sun.javafx.text.PrismTextLayout.getCaretShape(PrismTextLayout.java:317) ~[jfxrt.jar:?]
	at javafx.scene.text.Text$TextAttribute$11.computeValue(Text.java:1787) ~[jfxrt.jar:?]
	at javafx.scene.text.Text$TextAttribute$11.computeValue(Text.java:1777) ~[jfxrt.jar:?]
	at javafx.beans.binding.ObjectBinding.get(ObjectBinding.java:153) ~[jfxrt.jar:?]
	at javafx.beans.binding.ObjectExpression.getValue(ObjectExpression.java:50) ~[jfxrt.jar:?]
	at javafx.beans.property.ObjectPropertyBase.get(ObjectPropertyBase.java:132) ~[jfxrt.jar:?]
	at com.sun.javafx.scene.control.skin.TextFieldSkin.lambda$new$4(TextFieldSkin.java:233) ~[jfxrt.jar:?]
	at com.sun.javafx.binding.ExpressionHelper$SingleInvalidation.fireValueChangedEvent(ExpressionHelper.java:137) ~[jfxrt.jar:?]
	at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:81) ~[jfxrt.jar:?]
	at javafx.beans.property.ObjectPropertyBase.fireValueChangedEvent(ObjectPropertyBase.java:105) ~[jfxrt.jar:?]
	at javafx.beans.property.ObjectPropertyBase.markInvalid(ObjectPropertyBase.java:112) ~[jfxrt.jar:?]
	at javafx.beans.property.ObjectPropertyBase.access$000(ObjectPropertyBase.java:51) ~[jfxrt.jar:?]
	at javafx.beans.property.ObjectPropertyBase$Listener.invalidated(ObjectPropertyBase.java:233) ~[jfxrt.jar:?]
	at com.sun.javafx.binding.ExpressionHelper$SingleInvalidation.fireValueChangedEvent(ExpressionHelper.java:137) ~[jfxrt.jar:?]
	at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:81) ~[jfxrt.jar:?]
	at javafx.beans.binding.ObjectBinding.invalidate(ObjectBinding.java:172) ~[jfxrt.jar:?]
	at javafx.scene.text.Text.impl_geomChanged(Text.java:769) ~[jfxrt.jar:?]
	at javafx.scene.text.Text.needsTextLayout(Text.java:194) ~[jfxrt.jar:?]
	at javafx.scene.text.Text.needsFullTextLayout(Text.java:189) ~[jfxrt.jar:?]
	at javafx.scene.text.Text.access$200(Text.java:95) ~[jfxrt.jar:?]
	at javafx.scene.text.Text$2.invalidated(Text.java:389) ~[jfxrt.jar:?]
	at javafx.beans.property.StringPropertyBase.markInvalid(StringPropertyBase.java:109) ~[jfxrt.jar:?]
	at javafx.beans.property.StringPropertyBase.access$000(StringPropertyBase.java:49) ~[jfxrt.jar:?]
	at javafx.beans.property.StringPropertyBase$Listener.invalidated(StringPropertyBase.java:230) ~[jfxrt.jar:?]
	at com.sun.javafx.binding.ExpressionHelper$SingleInvalidation.fireValueChangedEvent(ExpressionHelper.java:137) ~[jfxrt.jar:?]
	at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:81) ~[jfxrt.jar:?]
	at javafx.beans.binding.StringBinding.invalidate(StringBinding.java:171) ~[jfxrt.jar:?]
	at com.sun.javafx.binding.BindingHelperObserver.invalidated(BindingHelperObserver.java:51) ~[jfxrt.jar:?]
	at com.sun.javafx.binding.ExpressionHelper$Generic.fireValueChangedEvent(ExpressionHelper.java:349) ~[jfxrt.jar:?]
	at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:81) ~[jfxrt.jar:?]
	at javafx.scene.control.TextInputControl$TextProperty.fireValueChangedEvent(TextInputControl.java:1389) ~[jfxrt.jar:?]
	at javafx.scene.control.TextInputControl$TextProperty.markInvalid(TextInputControl.java:1393) ~[jfxrt.jar:?]
	at javafx.scene.control.TextInputControl$TextProperty.set(TextInputControl.java:1324) ~[jfxrt.jar:?]
	at javafx.scene.control.TextInputControl.setText(TextInputControl.java:349) ~[jfxrt.jar:?]
	at org.jabref.gui.search.GlobalSearchBar.clearSearch(GlobalSearchBar.java:328) ~[JabRef-4.3.1.jar:?]
	at org.jabref.gui.search.GlobalSearchBar.performSearch(GlobalSearchBar.java:356) ~[JabRef-4.3.1.jar:?]
	at org.jabref.gui.BasePanel$SearchListener.listen(BasePanel.java:2095) ~[JabRef-4.3.1.jar:?]
	at sun.reflect.GeneratedMethodAccessor14.invoke(Unknown Source) ~[?:?]
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:1.8.0_222]
	at java.lang.reflect.Method.invoke(Method.java:498) ~[?:1.8.0_222]
	at com.google.common.eventbus.Subscriber.invokeSubscriberMethod(Subscriber.java:87) ~[JabRef-4.3.1.jar:?]
	at com.google.common.eventbus.Subscriber$SynchronizedSubscriber.invokeSubscriberMethod(Subscriber.java:144) ~[JabRef-4.3.1.jar:?]
	at com.google.common.eventbus.Subscriber$1.run(Subscriber.java:72) ~[JabRef-4.3.1.jar:?]
	at com.google.common.util.concurrent.MoreExecutors$DirectExecutor.execute(MoreExecutors.java:398) ~[JabRef-4.3.1.jar:?]
	at com.google.common.eventbus.Subscriber.dispatchEvent(Subscriber.java:67) ~[JabRef-4.3.1.jar:?]
	at com.google.common.eventbus.Dispatcher$PerThreadQueuedDispatcher.dispatch(Dispatcher.java:108) ~[JabRef-4.3.1.jar:?]
	at com.google.common.eventbus.EventBus.post(EventBus.java:212) ~[JabRef-4.3.1.jar:?]
	at org.jabref.model.database.BibDatabase.relayEntryChangeEvent(BibDatabase.java:582) ~[JabRef-4.3.1.jar:?]
	at sun.reflect.GeneratedMethodAccessor7.invoke(Unknown Source) ~[?:?]
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:1.8.0_222]
	at java.lang.reflect.Method.invoke(Method.java:498) ~[?:1.8.0_222]
	at com.google.common.eventbus.Subscriber.invokeSubscriberMethod(Subscriber.java:87) ~[JabRef-4.3.1.jar:?]
	at com.google.common.eventbus.Subscriber$SynchronizedSubscriber.invokeSubscriberMethod(Subscriber.java:144) ~[JabRef-4.3.1.jar:?]
	at com.google.common.eventbus.Subscriber$1.run(Subscriber.java:72) ~[JabRef-4.3.1.jar:?]
	at com.google.common.util.concurrent.MoreExecutors$DirectExecutor.execute(MoreExecutors.java:398) ~[JabRef-4.3.1.jar:?]
	at com.google.common.eventbus.Subscriber.dispatchEvent(Subscriber.java:67) ~[JabRef-4.3.1.jar:?]
	at com.google.common.eventbus.Dispatcher$PerThreadQueuedDispatcher.dispatch(Dispatcher.java:108) ~[JabRef-4.3.1.jar:?]
	at com.google.common.eventbus.EventBus.post(EventBus.java:212) ~[JabRef-4.3.1.jar:?]
	at org.jabref.model.entry.BibEntry.clearField(BibEntry.java:483) ~[JabRef-4.3.1.jar:?]
	at org.jabref.model.entry.BibEntry.clearField(BibEntry.java:455) ~[JabRef-4.3.1.jar:?]
	at org.jabref.migrations.MergeReviewIntoCommentMigration.updateFields(MergeReviewIntoCommentMigration.java:73) ~[JabRef-4.3.1.jar:?]
	at org.jabref.migrations.MergeReviewIntoCommentMigration.migrate(MergeReviewIntoCommentMigration.java:66) ~[JabRef-4.3.1.jar:?]
	at org.jabref.migrations.MergeReviewIntoCommentMigration.lambda$performMigration$2(MergeReviewIntoCommentMigration.java:32) ~[JabRef-4.3.1.jar:?]
	at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183) ~[?:1.8.0_222]
	at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175) ~[?:1.8.0_222]
	at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175) ~[?:1.8.0_222]
	at java.util.Iterator.forEachRemaining(Iterator.java:116) ~[?:1.8.0_222]
	at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801) ~[?:1.8.0_222]
	at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482) ~[?:1.8.0_222]
	at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472) ~[?:1.8.0_222]
	at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150) ~[?:1.8.0_222]
	at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173) ~[?:1.8.0_222]
	at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) ~[?:1.8.0_222]
	at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:485) ~[?:1.8.0_222]
	at org.jabref.migrations.MergeReviewIntoCommentMigration.performMigration(MergeReviewIntoCommentMigration.java:32) ~[JabRef-4.3.1.jar:?]
	at org.jabref.gui.importer.actions.MergeReviewIntoCommentAction.performAction(MergeReviewIntoCommentAction.java:21) ~[JabRef-4.3.1.jar:?]
	at org.jabref.gui.importer.actions.OpenDatabaseAction.performPostOpenActions(OpenDatabaseAction.java:93) ~[JabRef-4.3.1.jar:?]
	at org.jabref.JabRefGUI.openWindow(JabRefGUI.java:186) ~[JabRef-4.3.1.jar:?]
	at org.jabref.JabRefGUI.<init>(JabRefGUI.java:67) ~[JabRef-4.3.1.jar:?]
	at org.jabref.JabRefMain.lambda$start$1(JabRefMain.java:128) ~[JabRef-4.3.1.jar:?]
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) [?:1.8.0_222]
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) [?:1.8.0_222]
	at java.awt.EventQueue.access$500(EventQueue.java:97) [?:1.8.0_222]
	at java.awt.EventQueue$3.run(EventQueue.java:709) [?:1.8.0_222]
	at java.awt.EventQueue$3.run(EventQueue.java:703) [?:1.8.0_222]
	at java.security.AccessController.doPrivileged(Native Method) [?:1.8.0_222]
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74) [?:1.8.0_222]
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) [?:1.8.0_222]
	at org.GNOME.Accessibility.AtkWrapper$6.dispatchEvent(AtkWrapper.java:715) [java-atk-wrapper.jar:?]
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205) [?:1.8.0_222]
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [?:1.8.0_222]
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [?:1.8.0_222]
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [?:1.8.0_222]
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [?:1.8.0_222]
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [?:1.8.0_222]




@Siedlerchr
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4.3.1 still requires java 8 and openjfx 8.
5.0 alpha and all newer releases require java 11.

Please not that we lack resources to support more than the most current master version.
Ubuntu apt package has the very old 3.8 version I think.

Alternatively you can also install the snap version of JabRef:
https://snapcraft.io/jabref (edge for the latest master release)

Siedlerchr added a commit that referenced this issue Mar 14, 2021
30fb68e Create BJEDIS-ABNT-Number (#5255)
aafb868 Update geochimica-et-cosmochimica-acta.csl (#5321)
60ba25f british-journal-of-anaesthesia.csl: add comma delimiter between non-sequential citations eg. 1 4 7-9 -> 1, 4, 7-9  (#5313)
67e6564 Reindent/reorder (#5318)
c0d2a39 Ruby 3.0.0 (#5309)
76d60ff Update harvard-anglia-ruskin-university.csl (#5310)
bc18ac9 Create journal-for-the-study-of-the-new-testament.csl (#5312)
aff602c Update journal-of-food-protection.csl (#5315)
4503826 Update muscle-and-nerve.csl (#5317)
3bed58e constant redefinition
4d718a0 update documentaiton link
fa99e2f add comma delimiter between succesive numbers
d396f8b Allow privileged testing of PRs (#5307)
43b22c7 Update masarykova-univerzita-pravnicka-fakulta.csl, pravnik.csl, iso690-full-note-cs.csl (#5308)
8a31c1e Update copernicus-publications.csl (#5303)
96760bb Update anabases.csl (#5304)
744de6d removed locale (#5300)
7eb0d60 Update aviation-space-and-environmental-medicine.csl (#5297)
2769970 Update ruhr-universitat-bochum-lehrstuhl-fur-industrial-sales-and-ser… (#5298)
51e3f4c Update harvard-university-of-bath.csl (#5299)
5fce84f Create cns-spectrums.csl (#5290)
bb8082c Create journal-of-surgical-oncology.csl (#5259)
90c13ae Update ruhr-universitat-bochum-lehrstuhl-fur-industrial-sales-and-ser… (#5288)
4bab1ad Update early-christianity.csl (#5289)
636ba78 Update tatup-zeitschrift-fur-technikfolgenabschatzung-in-theorie-und-… (#5291)
b7cc511 Create biotechnologia.csl (#5292)
5bab881 Update journal-of-orthopaedic-trauma.csl (#5287)
5943413 Fix locales (#5285)
302bd65 Update universite-du-quebec-a-montreal-departement-dhistoire.csl (#5286)
860ae48 Add Haaga-Helia University of Applied Sciences Harvard style (#5282)
c1c27de  Localize Metropolia style title (#5283)
508da89 Fix presentation for Methods of Information in Medicine (#5284)
53e1d0b Create geschichte-und-gesellschaft.csl (#5216)
d7ed0cb Create universite-de-geneve-departement-de-francais-moderne.csl (#5212)
80c404b Update journal-of-orthopaedic-trauma.csl (#5281)
20c143a Adding publishers' names (#5280)
6e5cd59 Update sodertorns-hogskola-oxford.csl (#5279)
52f2621 dollar-brace
a260294 Create journal-of-microbiology-and-biotechnology.csl (#5277)
1fc979e Create qeios.csl (#5261)
86347b7 GH does this for us -- again, sorry guys
b649589 Create experimental-biology-and-medicine.csl (#5276)
12ae0b1 Revert "tell sheldon about the job state"
bdcae89 tell sheldon about the job state
1240067 Add Vegetation classification and Survey (#5271)
6f398f0 Major update to Gallia.csl (#5269)
2a74b2c Update filters.yaml (#5273)
20046d2 Update spec_helper.rb (#5272)
2ee0dd8 Create the-sociological-review.csl (#5260)
5b8d09c move filters to inert file to pacify Sheldon (#5268)
e5f3315 Localize more language descriptors in style titles (#5270)
bfd2942 Localize more language descriptors in style titles (#5267)
35e276f Fix variable used for the label after indication of number of pages (#5240)
60f6371 Create Universidade-do-Estado-do-Rio-de-Janeiro.csl (#5247)
d8cc2ae Create the-journal-of-the-acoustical-society-of-america-numeric.csl (#5256)
92259c1 Create journal-of-financial-and-quantitative-analysis.csl (#5264)
6ba8aab Create journal-of-vestibular-research.csl (#5258)
0c88f41 Update european-journal-of-international-law.csl (#5265)
cff5abc Put language descriptor within parentheses
4a62709 Update monash-university-harvard.csl (#5253)
64fd1aa Localize more language descriptors in style titles (#5262)
f6519cb Localize more language descriptors in style titles (#5257)
170ccae tiny fixes for universitat-basel-iberoromanistik.csl (#5254)
b7284c9 Localize more language descriptors in style titles (#5252)
f4ef858 Add "Baishideng Publishing Group" dependents (#5251)
266e7c3 Make world-journal-of-hepatology.csl to bpg.csl parent (#5243)
9129098 fix small formatting issues for mclc.csl (#5229)
5d9560b Create crispr-journal.csl (#5249)
a217299 Change "Czech" to "Čeština" in titles (#5248)
4fef39a Create journal-of-open-research-software.csl (#5245)
2bff1a6 Change "Dutch" to "Nederlands" in titles (#5242)
f28da34 Update spec_helper.rb (#5246)
e0e977c Move content from wiki pages to markdown files (#5194)
018304c Update universite-de-montreal-apa.csl (#5239)
3b83e5c Create sodertorns-hogskola-oxford.csl (#5234)
1335378 Stop notifying 8827 port on Zotero servers (#5237)
f079b2a Update author-year disambiguation (#5238)
60bb0c9 Update technische-universitat-dresden-medizin.csl (#5236)
e374657 Create Leidraad voor juridische auteurs 2019 (Dutch) (#5223)
0450d89 Add new style for U of Mannheim, Germanistische Linguistik (#5228)
81f0689 Create health-sports-rehabilitation-medicine.csl (#5233)
c152a44 Update Gemfile.lock (#5235)
748e1eb Update geochimica-et-cosmochimica-acta.csl (#5231)
06b9ce8 Update zeitschrift-fur-theologie-und-philosophie.csl (#5230)
e747cb1 haute-ecole-de-gestion-de-geneve: Make polyglot & et al changes
4cfedb7 Create universite-de-sherbrooke-histoire.csl (#5210)
a96a61e Update journal-of-glaciology.csl (#5222)
c6a94c9 Add Journal of Human Rights (#5227)
c5c9c5f Update ruhr-universitat-bochum-lehrstuhl-fur-industrial-sales-and-ser… (#5214)
ffb7aa6 Create comparativ.csl (#5215)
e07329a Update lancaster-university-harvard.csl (#5220)
c075d41 Update mimesis-edizioni.csl (#5219)
502970a Removed space in year only citation (#5218)
13e8c6b Update acta-scientiae-veterinariae.csl (#5209)
0699da6 Remake mammallia.csl for Oct/2020 guidelines. (#5207)
b2dd3fd Update journal-of-international-business-studies.csl (#5217)
dd52bfe Update quaternaire.csl (#5199)
ccb1b0d rebuild webpage and article-journal citations in journal-of-forensic-sciences.csl (#5203)
f02f4fb Create pedosphere.csl (#5196)
70dd87a Create open-gender-journal.csl (#5198)
d272998 Create the-quarterly-journal-of-economics.csl (#5197)
d27cab3 fix locale issues, add cite-locator (#5206)

git-subtree-dir: buildres/csl/csl-styles
git-subtree-split: 30fb68e
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