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

gnu/local.mk

@@ -1511,6 +1511,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/java-apache-ivy-port-to-latest-bouncycastle.patch	\
   %D%/packages/patches/java-commons-collections-fix-java8.patch \
   %D%/packages/patches/java-commons-lang-fix-dependency.patch \
+  %D%/packages/patches/java-guava-remove-annotation-deps.patch \
   %D%/packages/patches/java-jeromq-fix-tests.patch		\
   %D%/packages/patches/java-openjfx-build-jdk_version.patch     \
   %D%/packages/patches/java-powermock-fix-java-files.patch		\

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

gnu/packages/java.scm

@@ -6249,8 +6249,7 @@ used by programmers to guide the static analysis.")
 (define-public java-guava
   (package
     (name "java-guava")
-    ;; This is the last release of Guava that can be built with Java 7.
+    (version "31.1")
-    (version "20.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -6259,7 +6258,9 @@ used by programmers to guide the static analysis.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "00h5cawdjic1vind3yivzh1f58flvm1yfmhsyqwyvmbvj1vakysp"))))
+                "0sv1w5cnids9ad3l7qhrh3dh1wdqwc946iinsxryafr25wg5z1lp"))
+              (patches
+               (search-patches "java-guava-remove-annotation-deps.patch"))))
     (build-system ant-build-system)
     (arguments
      `(#:tests? #f                      ; no tests included
@@ -6273,27 +6274,26 @@ used by programmers to guide the static analysis.")
                ;; Remove annotations to avoid extra dependencies:
                ;; * "j2objc" annotations are used when converting Java to
                ;;   Objective C;
-               ;; * "errorprone" annotations catch common Java mistakes at
-               ;;   compile time;
                ;; * "IgnoreJRERequirement" is used for Android.
+               ;; * "Nullable" is used to catch NPE at build time.
                (substitute* (find-files "." "\\.java$")
                  (("import com.google.j2objc.*") "")
-                 (("import com.google.errorprone.annotation.*") "")
+                 (("import org.checkerframework.checker.*") "")
-                 (("import org.codehaus.mojo.animal_sniffer.*") "")
+                 (("@ReflectionSupport.*") "")
-                 (("@CanIgnoreReturnValue") "")
-                 (("@LazyInit") "")
                  (("@WeakOuter") "")
                  (("@RetainedWith") "")
                  (("@Weak") "")
-                 (("@ForOverride") "")
                  (("@J2ObjCIncompatible") "")
-                 (("@IgnoreJRERequirement") "")))
+                 (("@IgnoreJRERequirement") "")
-             #t))
+                 (("@Nullable") "")))))
+         ;; This is required by guava, but this is just an empty stub
+         (add-before 'install 'install-listenablefuture-stub
+           (install-pom-file "futures/listenablefuture9999/pom.xml"))
          (replace 'install (install-from-pom "guava/pom.xml")))))
     (inputs
-     (list java-jsr305))
+     (list java-error-prone-annotations java-jsr305))
     (propagated-inputs
-     (list java-guava-parent-pom))
+     (list java-guava-futures-failureaccess java-guava-parent-pom))
     (home-page "https://github.com/google/guava")
     (synopsis "Google core libraries for Java")
     (description "Guava is a set of core libraries that includes new
@@ -6303,6 +6303,21 @@ concurrency, I/O, hashing, primitives, reflection, string processing, and much
 more!")
     (license license:asl2.0)))
 
+(define-public java-guava-futures-failureaccess
+  (package
+    (inherit java-guava)
+    (name "java-guava-futures-failureaccess")
+    (arguments
+     `(#:tests? #f; no tests
+       #:jar-name "guava-futures-failureaccess.jar"
+       #:source-dir "futures/failureaccess/src"
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'install
+           (install-from-pom "futures/failureaccess/pom.xml")))))
+    (propagated-inputs
+     `(("java-sonatype-oss-parent-pom" ,java-sonatype-oss-parent-pom-7)))))
+
 (define java-guava-parent-pom
   (package
     (inherit java-guava)

gnu/packages/maven.scm

@@ -2170,7 +2170,8 @@ layer for plugins that need to keep Maven2 compatibility.")))
                      "java-javax-inject" "java-plexus-component-annotations"
                      "java-plexus-utils" "java-plexus-interpolation"
                      "java-plexus-sec-dispatcher" "java-plexus-cipher" "java-guava"
-                     "java-jansi" "java-jsr250" "java-cdi-api" "java-commons-cli"
+                     "java-guava-futures-failureaccess" "java-jansi"
+                     "java-jsr250" "java-cdi-api" "java-commons-cli"
                      "java-commons-io" "java-commons-lang3" "java-slf4j-api"))))
              (substitute* "apache-maven/src/bin/mvn"
                (("cygwin=false;")
@@ -2239,6 +2240,7 @@ layer for plugins that need to keep Maven2 compatibility.")))
            java-plexus-sec-dispatcher
            java-plexus-cipher
            java-guava
+           java-guava-futures-failureaccess
            java-jansi
            java-jsr250
            java-cdi-api

gnu/packages/patches/java-guava-remove-annotation-deps.patch

@@ -0,0 +1,37 @@
+From 41d216ca7993991d32a077d0650ccfad8a846942 Mon Sep 17 00:00:00 2001
+From: Julien Lepiller <julien@lepiller.eu>
+Date: Sat, 25 Feb 2023 10:02:11 +0100
+Subject: [PATCH] Remove annotation dependencies
+
+This is used to prevent a failure when guix creates the Maven directory
+structure and fails to find these dependencies.
+---
+ guava/pom.xml | 12 ------------
+ 1 file changed, 12 deletions(-)
+
+diff --git a/guava/pom.xml b/guava/pom.xml
+index 81a2005..5237047 100644
+--- a/guava/pom.xml
++++ b/guava/pom.xml
+@@ -31,18 +31,6 @@
+       <groupId>com.google.code.findbugs</groupId>
+       <artifactId>jsr305</artifactId>
+     </dependency>
+-    <dependency>
+-      <groupId>org.checkerframework</groupId>
+-      <artifactId>checker-qual</artifactId>
+-    </dependency>
+-    <dependency>
+-      <groupId>com.google.errorprone</groupId>
+-      <artifactId>error_prone_annotations</artifactId>
+-    </dependency>
+-    <dependency>
+-      <groupId>com.google.j2objc</groupId>
+-      <artifactId>j2objc-annotations</artifactId>
+-    </dependency>
+     <!-- TODO(cpovirk): does this comment belong on the <dependency> in <profiles>? -->
+     <!-- TODO(cpovirk): want this only for dependency plugin but seems not to work there? Maven runs without failure, but the resulting Javadoc is missing the hoped-for inherited text -->
+   </dependencies>
+-- 
+2.38.1
+