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| author | Julien Lepiller <julien@lepiller.eu> | 2023-02-25 21:30:29 +0100 |
|---|---|---|
| committer | Julien Lepiller <julien@lepiller.eu> | 2024-04-20 18:31:34 +0200 |
| commit | 7ce7464934aa9ba26b4ec2708c964af7b1d0deb2 (patch) | |
| tree | c773171dd9f63b528c41c9764673aca3f2bb8e63 /gnu/packages/bioinformatics.scm | |
| parent | f1ed3d4699a726cd13985afa32b9c97e72505970 (diff) | |
gnu: java-guava: Update to 31.1.
* gnu/packages/patches/java-guava-remove-annotation-deps.patch: New
file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/java.scm (java-guava): Update to 31.1.
[source]: Use patch.
(java-guava-futures-failureaccess): New variable.
* gnu/packages/bioinformatics.scm (java-picard, java-picard-2.10.3): Fix for
newer guava.
* gnu/packages/maven.scm (maven): Add java-guava-futures-failureaccess.
Change-Id: Id2553c48e11c6001fb45a0589720cef1551804d9
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 8 |
1 files changed, 8 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 448ea5d6de..c2e9f209bc 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7303,6 +7303,10 @@ geographic distributions.") (modify-phases %standard-phases ;; FIXME: this phase fails with "duplicate entry: htsjdk/samtools/AbstractBAMFileIndex$1.class" (delete 'generate-jar-indices) + (add-after 'unpack 'fix-guava + (lambda _ + (substitute* "src/java/picard/cmdline/CommandLineParser.java" + (("CharMatcher.ASCII") "CharMatcher.ascii()")))) (add-after 'unpack 'use-our-htsjdk (lambda* (#:key inputs #:allow-other-keys) (substitute* "build.xml" @@ -7362,6 +7366,10 @@ VCF.") (delete 'generate-jar-indices) (add-after 'unpack 'remove-useless-build.xml (lambda _ (delete-file "build.xml") #t)) + (add-after 'unpack 'fix-guava + (lambda _ + (substitute* "src/main/java/picard/cmdline/CommandLineParser.java" + (("CharMatcher.ASCII") "CharMatcher.ascii()")))) ;; This is necessary to ensure that htsjdk is found when using ;; picard.jar as an executable. (add-before 'build 'edit-classpath-in-manifest |