From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp0 ([2001:41d0:8:6d80::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms0.migadu.com with LMTPS id SIHFOWqs8WAyRAEAgWs5BA (envelope-from ) for ; Fri, 16 Jul 2021 17:57:30 +0200 Received: from aspmx1.migadu.com ([2001:41d0:8:6d80::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp0 with LMTPS id EH1+NWqs8WA8YgAA1q6Kng (envelope-from ) for ; Fri, 16 Jul 2021 15:57:30 +0000 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id A6C672BC9F for ; Fri, 16 Jul 2021 17:57:30 +0200 (CEST) Received: from localhost ([::1]:39792 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1m4QDR-0005WT-Pp for larch@yhetil.org; Fri, 16 Jul 2021 11:57:29 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41642) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1m4QD1-0004kb-Ra for guix-patches@gnu.org; Fri, 16 Jul 2021 11:57:04 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:40645) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1m4QD1-0007Wx-Gj for guix-patches@gnu.org; Fri, 16 Jul 2021 11:57:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1m4QD1-00038T-Gw for guix-patches@gnu.org; Fri, 16 Jul 2021 11:57:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#49597] [PATCH core-updates 14/15] gnu: Use 'search-input-file' when looking for .jar files. Resent-From: Ludovic =?UTF-8?Q?Court=C3=A8s?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 16 Jul 2021 15:57:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 49597 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 49597@debbugs.gnu.org Cc: Ludovic =?UTF-8?Q?Court=C3=A8s?= Received: via spool by 49597-submit@debbugs.gnu.org id=B49597.162645098111971 (code B ref 49597); Fri, 16 Jul 2021 15:57:03 +0000 Received: (at 49597) by debbugs.gnu.org; 16 Jul 2021 15:56:21 +0000 Received: from localhost ([127.0.0.1]:52185 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1m4QCK-00036u-E6 for submit@debbugs.gnu.org; Fri, 16 Jul 2021 11:56:20 -0400 Received: from eggs.gnu.org ([209.51.188.92]:43552) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1m4QC4-00034m-6w for 49597@debbugs.gnu.org; Fri, 16 Jul 2021 11:56:05 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:33774) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1m4QBy-0006Wi-Ux; Fri, 16 Jul 2021 11:55:58 -0400 Received: from vpn-0-27.aquilenet.fr ([2a0c:e300:4:27::]:38216 helo=gnu.org) by fencepost.gnu.org with esmtpsa (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1m4QBx-0004IN-Eq; Fri, 16 Jul 2021 11:55:58 -0400 From: Ludovic =?UTF-8?Q?Court=C3=A8s?= Date: Fri, 16 Jul 2021 17:54:19 +0200 Message-Id: <20210716155420.32447-14-ludo@gnu.org> X-Mailer: git-send-email 2.32.0 In-Reply-To: <20210716155420.32447-1-ludo@gnu.org> References: <20210716155420.32447-1-ludo@gnu.org> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Migadu-Flow: FLOW_IN ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1626451050; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-transfer-encoding:content-transfer-encoding:resent-cc: resent-from:resent-sender:resent-message-id:in-reply-to:in-reply-to: references:references:list-id:list-help:list-unsubscribe: list-subscribe:list-post; bh=1HoYQFgKQQnVuoumMivcOWj7ilmzr1nrTUEJncCrsj8=; b=VlvAsNvSlPrZAVQCbi92+L9OufyXhg3vkZYIQX7Vt/TGLVCmIBiE32qq/xCkit/n6OYUS2 H0MIQcTmlMOKeggInx0etgCkcRiegdR6Wx9l1wjxO0PgBGpsqDmifnrv46wpsWpYphRf5P o5ZerJ//uufWfHc5i5dgz2n+IVkHHPRo5EGtR+1Bpo9JoV6vHX0RZfNAWvVlHEd2m64NuA 0Xreeo1iSI/R3vTEcjK0LYCDpwDgmThUcgl/vkv69Y3miKrcl/gxsuW0tqg5ECmLxAd4sM b78OudnfXGf1J8SqgNF66C2Ul8FE69kg4nAcuDUo5n3mY55pODG1NIWDWK8naQ== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1626451050; a=rsa-sha256; cv=none; b=hze6JAm5cMTdOjjetLQIBkmCcBzujPesN5Qf0wOvU7Wp1v7TlWa33S8eglEWP4zP8APRZe qKHw3k1tqT1TAltjWtNbrRQl5icb3Z2gdZzgjuyysAgQcOYssOg3F/DVYDNDWVI9Q0BuVn cygpj+Ca5X9N4nJE2CPvUrnV4pIPdlAKz6CQZA+n8C7850jPMaXTRFHRtFJNtbWXXqCYoA Sq7HRZtG3JVEuMSTjDE9XF9FgXibpo8RegaLq8IPnBcWwnOaX8+kTaTRsVZflpskdu4xVH ZW4DGe8lf9rpWh+jfN4hurQDKGq3jF8ocvz7aIpzxX+1HxHKp3r6sPpEYYA/7w== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=none; spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Spam-Score: 2.09 Authentication-Results: aspmx1.migadu.com; dkim=none; dmarc=pass (policy=none) header.from=gnu.org; spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Queue-Id: A6C672BC9F X-Spam-Score: 2.09 X-Migadu-Scanner: scn0.migadu.com X-TUID: 1Bl1VGFg8W8p * gnu/packages/bioinformatics.scm (java-picard-1.113): Use 'search-input-file' when looking for *.jar. (fastqc): Likewise. * gnu/packages/groovy.scm (groovy): Likewise. * gnu/packages/java.scm (ant-bootstrap): Likewise. (ecj-bootstrap): Likewise. (java-cisd-base): Likewise. (java-cisd-args4j): Likewise. (java-cisd-jhdf5): Likewise. (java-native-access): Likewise. (java-native-access-platform): Likewise. * gnu/packages/maths.scm (hdf-java): Likewise. --- gnu/packages/bioinformatics.scm | 20 ++++----- gnu/packages/groovy.scm | 2 +- gnu/packages/java.scm | 76 +++++++++++++++++---------------- gnu/packages/maths.scm | 3 +- 4 files changed, 49 insertions(+), 52 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d57c00a451..7a8e5f16c0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4379,9 +4379,7 @@ VCF.") (lambda* (#:key inputs #:allow-other-keys) (substitute* "build.xml" (("\\$\\{lib\\}/apache-ant-1.8.2-bzip2.jar") - (string-append (assoc-ref inputs "ant") - "/lib/ant.jar"))) - #t)) + (search-input-file inputs "/lib/ant.jar"))))) (add-after 'unpack 'make-test-target-independent (lambda* (#:key inputs #:allow-other-keys) (substitute* "build.xml" @@ -4478,15 +4476,13 @@ VCF.") (lambda* (#:key inputs #:allow-other-keys) (substitute* "build.xml" (("jbzip2-0.9.jar") - (string-append (assoc-ref inputs "java-jbzip2") - "/share/java/jbzip2.jar")) + (search-input-file inputs "/share/java/jbzip2.jar")) (("sam-1.103.jar") - (string-append (assoc-ref inputs "java-picard-1.113") - "/share/java/sam-1.112.jar")) + (search-input-file inputs + "/share/java/sam-1.112.jar")) (("cisd-jhdf5.jar") - (string-append (assoc-ref inputs "java-cisd-jhdf5") - "/share/java/sis-jhdf5.jar"))) - #t)) + (search-input-file inputs + "/share/java/sis-jhdf5.jar"))))) ;; There is no installation target (replace 'install (lambda* (#:key inputs outputs #:allow-other-keys) @@ -9137,8 +9133,8 @@ browser.") (substitute* "bin/linux/fseq" (("java") (which "java")) (("\\$REALDIR/../lib/commons-cli-1.1.jar") - (string-append (assoc-ref inputs "java-commons-cli") - "/share/java/commons-cli.jar")) + (search-input-file inputs + "/share/java/commons-cli.jar")) (("REALDIR=.*") (string-append "REALDIR=" bin "\n"))) (install-file "README.txt" doc) diff --git a/gnu/packages/groovy.scm b/gnu/packages/groovy.scm index c44a17b59e..73a62e1045 100644 --- a/gnu/packages/groovy.scm +++ b/gnu/packages/groovy.scm @@ -827,7 +827,7 @@ and modify groovy's @dfn{Abstract Syntax Tree} (AST).")))) "java-jansi" "java-jline-2")) ;; antlr.jar is present twice in antlr2. Symlink doesn't like ;; it, so we symlink it here. - (symlink (string-append (assoc-ref inputs "antlr2") "/lib/antlr.jar") + (symlink (search-input-file inputs "/lib/antlr.jar") (string-append out-lib "/antlr.jar")) (for-each (lambda (tool) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index fdfd044926..f4a426e559 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -382,8 +382,7 @@ JNI.") (setenv "JAVAC" (search-input-file inputs "/bin/jikes")) (setenv "CLASSPATH" - (string-append (assoc-ref inputs "jamvm") - "/lib/rt.jar")) + (search-input-file inputs "/lib/rt.jar")) ;; Ant complains if this file doesn't exist. (setenv "HOME" "/tmp") @@ -486,8 +485,7 @@ build process and its dependencies, whereas Make uses Makefile format.") (lambda* (#:key inputs #:allow-other-keys) (setenv "CLASSPATH" (string-join - (cons (string-append (assoc-ref inputs "jamvm") - "/lib/rt.jar") + (cons (search-input-file inputs "/lib/rt.jar") (find-files (string-append (assoc-ref inputs "ant-bootstrap") "/lib") @@ -3221,19 +3219,22 @@ Main-Class: org.eclipse.jdt.internal.compiler.batch.Main\n" (lambda* (#:key inputs #:allow-other-keys) (substitute* "build/build.xml" (("\\$\\{lib\\}/testng/testng-jdk15.jar") - (string-append (assoc-ref inputs "java-testng") - "/share/java/java-testng.jar")) + (search-input-file inputs + "/share/java/java-testng.jar")) (("\\$\\{lib\\}/commons-lang/commons-lang.jar") - (string-append (assoc-ref inputs "java-commons-lang") - "/share/java/commons-lang-" - ,(package-version java-commons-lang) ".jar")) + (search-input-file inputs + (string-append + "/share/java/commons-lang-" + ,(package-version java-commons-lang) + ".jar"))) (("\\$\\{lib\\}/commons-io/commons-io.jar") - (string-append (assoc-ref inputs "java-commons-io") - "/lib/m2/commons-io/commons-io/" - ,(package-version java-commons-io) - "/commons-io-" - ,(package-version java-commons-io) - ".jar")) + (search-input-file inputs + (string-append + "/lib/m2/commons-io/commons-io/" + ,(package-version java-commons-io) + "/commons-io-" + ,(package-version java-commons-io) + ".jar"))) ;; Remove dependency on svn (("