JabRef not working on Arch Linux #5299
Comments
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I also experience this under windows when I use the jar. @tobiasdiez any idea? |
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With modularized Java 11 applications, the |
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Thanks to both of you for your fast responses. @tobiasdiez, I can confirm that running compiles and runs JabRef without any problems. However, I cannot make it work with when working under the source tree. The command gives the following error this time: When I run I am assuming that
I would appreciate if you provided a minimal working example. Then, I can write a |
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Final comment... As of 18cf80f, the following Basically, after |
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Thanks for the update. That size is indeed huge, I found out that this is somehow a linux issue with jlink and that there is a workaround for reducing the size: |
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@aytekinar It should suffice to use what is inside of |
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@Siedlerchr I will try to do the manual stripping. However, Arch Linux also does stripping when packaging binaries. @tobiasdiez I would appreciate if you could write an MWE for that. I can get rid of the |
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I have no linux at hand, so I cannot give more details sorry. On Windows, the |
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Update 1. Stripping the image manually as suggested by @Siedlerchr, as of a357bbd, still results in 705.38 MiB. Update 2. and its size is In fact, #!/bin/sh
DIR="${0%/*}"
"$DIR/java" -p "$DIR/../app" -m org.jabref/org.jabref.JabRefLauncher "$@"which uses the In short,
That said, I think this issue is not open anymore. Anybody with a problem on Arch Linux can see the solution you have suggested and either use my Edit. For your reference, the package size has the following distribution among the package's modules/directories: |
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There is already one maintaining an Arch repo for jabref: (I think it's @j0hannes ) It would be nice if someone of you could then update the installation instructions page in the help |
I am aware of that package. Unfortunately, I am right now writing a paper and I cannot open my bibliography files (well, yes, I can open them in text editors, but you know...). If you check the latest comment, @j0hannes is still testing Java 11 issues. In the meantime, I needed to write mine.
There is no need to update Arch and Manjaro part. Because I am not pushing my Edit. In fact, there might be a small update later to the statement:
if @j0hannes decides to borrow my solution (i.e., building from source). |
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Hi,
I released a new PKGBUILD the day after that comment. Since then, it's working fine for me.
I actually wouldn't do that since I wrote the AUR package specifically to avoid doing the compilation with gradle, which I found rather annoying for several reasons. It also failed to build frequently. I never had a problem with the pre-compiled jar so far -- apart from bugs in the application itself. You might want to contribute to jabref-git instead. |
Just now I have run When I try to run JabRef from dmenu (desktop file) it does not open anything (I am running which brings me back to my first comment above and which, as @tobiasdiez mentions in his comment, is expected:
This was the reason why I needed to write a new Anyways... Thank you for your prompt response and making your points. Cheers. |
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Ok, I think it should be sufficient to package only to This should reduce the size of the package considerably. (For example, As a side note, I will experiment with jpackage during the next days. This should give |
Thanks for pointing that out. I wasn't aware of it. What is the point of offering jar files in https://builds.jabref.org/master/ then? I am supposed to download them, decompose them and run gradle on them? That doesn't sound like a solution for everybody.
I'm happy about any suggestion how to use the jar file provided by builds.jabref.org without executing it with java. |
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We have only recently discovered that the |
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I will try to look into it today. |
So it broke recently? Because I'm still able to run the version installed a week ago. |
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Could anyone of you try if the .sh script works? (I currently don't have a linux system at hand) |
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It runs, and open a graphical installer that looks like the ones that Windows has. I canceled it when it wanted to write to system directories; which is not possible for a regular user and I would never execute a script like that with root. I looked into the code and there seems to be no other option than running that installer. So, from my point of view, it's of little use for linux users. I don't see how to use it for packaging Jabref. |
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I totally agree with @j0hannes on the shell-script solution. IMHO, you (devs) should just help package maintainers write their own scripts to package your applications. I mean, if I know how to build your application, it will be trivial for me to package it for my system. Not to mention the fact that graphical installers are a big problem for automated packaging processes. |
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Yes, I know that graphical installers are not the best solution for unix. It was just a try. |
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Once jpackager works, I do think we can completely get rid of intalll4j (also on Windows). That being said, I managed to add a build pipeline that produces a zip file of the
It would be nice if you could try this. If it works, then I'll add the necessary code to publish these zip files to |
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It runs. This is the log: |
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Debian packages are fine to convert; that might be the more reliable way. The filename will remain stable as it has been for the jar, right? |
* Update Installation.md Updated the installation procedure for JabRef 5.x and on. Following the [comment](JabRef/jabref#5299 (comment)) of @Siedlerchr. * Remove `deb` and `rpm` files
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So I've managed to make jpackage work on all platforms. @j0hannes @aytekinar what would be the most convenient distribution format for package maintainers and users on linux:
(one of the questions is if the last one is necessary or if the first two are actually sufficient). Refs: #5312 (comment) (you are invited to try out the builds referenced there) |
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@tobiasdiez IMHO, the last one is necessary and sufficient. Of course, Arch's packaging system knows how to interpret/unpack
For this reason, I think that |
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I tried to provide a working jabref-git PKGBUILD for Arch Linux, but it fails at the gradle jlink step. pkgname=jabref-git
pkgver=5.0alpha.r99.g381f0f3f08
pkgrel=1
pkgdesc="GUI frontend for BibTeX, written in Java -- built from git"
arch=('any')
url="https://www.jabref.org"
license=('MIT')
depends=('java-environment>=11' 'java11-openjfx')
makedepends=('git' 'gradle')
optdepends=('gsettings-desktop-schemas: For web search support')
provides=('jabref')
conflicts=('jabref')
source=("${pkgname%-git}::git+https://github.com/JabRef/jabref.git"
git+https://github.com/citation-style-language/locales.git
git+https://github.com/citation-style-language/styles.git
"${pkgname%-git}.desktop"
"${pkgname%-git}.sh")
md5sums=('SKIP'
'SKIP'
'SKIP'
'5f76feb6b2f66a2ea8b52bca999a934f'
'b7c7fca66fe7e0a466df1f6b3c0539ff')
pkgver() {
cd ${pkgname%-git}
git describe --tags | sed 's+-alpha-+alpha.r+'|cut -c2-|tr - .
}
prepare() {
cd ${pkgname%-git}
_release=$(sed -n 's/.*version = \"\(.*-dev\)\"/\1/p' build.gradle)
[[ -d locales ]] || ln -s ../locales locales
[[ -d styles ]] || ln -s ../styles styles
git submodule update --init
}
build() {
cd ${pkgname%-git}
gradle assemble
gradle jlink
}
# package() {
# cd ${pkgname%-git}
# find "${srcdir}/${pkgname%-git}/build/releases" \
# -iname "JabRef-${_release}.jar" \
# -exec install -Dm644 {} "$pkgdir"/usr/share/java/jabref/JabRef.jar \;
# install -Dm755 "$srcdir"/jabref.sh "$pkgdir"/usr/bin/jabref
# install -Dm644 "$srcdir"/jabref.desktop \
# "$pkgdir"/usr/share/applications/jabref.desktop
# install -Dm644 "build/resources/main/icons/${pkgname%-git}.svg" \
# "$pkgdir"/usr/share/pixmaps/${pkgname%-git}.svg
# install -Dm644 LICENSE.md "$pkgdir"/usr/share/licenses/${pkgname}/LICENSE
# }
package() {
cd "${srcdir}"
install -d "${pkgdir}/opt"
cp -R "${pkgname}/build" "${pkgdir}/opt/jabref"
install -D jabref.desktop "${pkgdir}/usr/share/applications/jabref.desktop"
install -D jabref.png "${pkgdir}/usr/share/pixmaps/jabref.desktop"
}this is the error message |
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@stefanhusmann, please check my PKGBUILD. It is building on my machine with |
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I checked it, an I get the same error message as with my PKGBUILD. |
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Please check if gradle is running under the correct java version: |
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gradlew picks the Gradle 5.6, which is coming with the jabref sources, but I also tried with gradle 5.6.2 which is coming with the official Arch Linux package. Gradle 5.6Build time: 2019-08-14 21:05:25 UTC Kotlin: 1.3.41 |
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Hello, I now was able to build jabref. It seems that sowehow the java11-openjfx (the system package delivered by Arch Linux) interferes with the build process. It needs to be uninstalled. JabRef is also launchable with /opt/jabref/bin/JabRefMain, but something still seems wrong: |
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The log4j error should be fixed in the latest master version. |
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@j0hannes Could you update the package? |
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@homocomputeris, I will, I have just been travelling for two weeks now. |
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@j0hannes Thanks a lot! |
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@homocomputeris, I have adapted the package, could you try? |
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@j0hannes Great, it works, thanks a lot!. which is a dependency, probably? It's also a bit laggy and slowish, but it's probably JabRef's problems. |
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@homocomputeris The logger issue is a known problem. We are working on it. |
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It turns out that in j0hannes's package the desktop entry still exists and this just works: which is fine for me ATM. |
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@homocomputeris, there should be a .desktop file: /usr/share/applications/JabRef.desktop |
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@j0hannes I have found it (see above) but it has old paths: |
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@homocomputeris, what do you mean by "old paths"? The icon is stored in /usr/share/pixmaps/ and doesn't need a full path here. On my machines, the icon is shown in the launcher, and clicking on it starts the application.
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@j0hannes Well, I don't know why it doesn't appear in my system's Gnome menu. I've reinstalled the package, and I have $ lsa /usr/share/applications/JabRef.desktop
-rw-r--r-- 1 root root 412 oct 15 12:46 /usr/share/applications/JabRef.desktop$ cat lsa /usr/share/applications/JabRef.desktop
[Desktop Entry]
Name=JabRef
GenericName=BibTeX Editor
Comment=JabRef is an open source bibliography reference manager. The native file format used by JabRef is BibTeX, the standard LaTeX bibliography format.
Type=Application
Terminal=false
Icon=JabRef
Exec=JabRef %U
Path=/opt/JabRef/bin
Keywords=bibtex;biblatex;latex;bibliography
Categories=Office;
StartupWMClass=org-jabref-JabRefMain
MimeType=text/x-bibtex; |
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@homocomputeris, according to this page it should work like that. |
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Does |
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In my case it doesn't; I did that check before pushing the new version. |
Your launcher is shown in the menu, so it's correct. |
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
I am on an Arch Linux machine with the following:
Steps to reproduce the behavior:
gradle releaseJarorgradle shadowJar(see log)java -jar build/releases/JabRef-5.0-dev.jarI have a failure with the following error:
Log File
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