From debbugs-submit-bounces@debbugs.gnu.org Wed Nov 22 06:22:32 2017 Received: (at submit) by debbugs.gnu.org; 22 Nov 2017 11:22:32 +0000 Received: from localhost ([127.0.0.1]:51892 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1eHT6u-0007ZR-3z for submit@debbugs.gnu.org; Wed, 22 Nov 2017 06:22:32 -0500 Received: from eggs.gnu.org ([208.118.235.92]:57975) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1eHT6r-0007ZB-BN for submit@debbugs.gnu.org; Wed, 22 Nov 2017 06:22:30 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1eHT6h-0007Ff-A1 for submit@debbugs.gnu.org; Wed, 22 Nov 2017 06:22:24 -0500 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,T_DKIM_INVALID autolearn=disabled version=3.3.2 Received: from lists.gnu.org ([2001:4830:134:3::11]:53786) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1eHT6h-0007Fb-6n for submit@debbugs.gnu.org; Wed, 22 Nov 2017 06:22:19 -0500 Received: from eggs.gnu.org ([2001:4830:134:3::10]:48854) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1eHT6a-0004Fx-Ol for guix-patches@gnu.org; Wed, 22 Nov 2017 06:22:18 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1eHT6V-0007BF-RB for guix-patches@gnu.org; Wed, 22 Nov 2017 06:22:12 -0500 Received: from pegasus.bbbm.mdc-berlin.de ([141.80.25.20]:39920) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1eHT6V-0007AR-HG for guix-patches@gnu.org; Wed, 22 Nov 2017 06:22:07 -0500 Received: from localhost (localhost [127.0.0.1]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 69109511B20 for ; Wed, 22 Nov 2017 12:22:04 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:message-id:date:date :subject:subject:from:from:user-agent:received:received :received; s=mdc; t=1511349719; x=1513164120; bh=C/nh+BgsYVt5Dek L3RP+YdUjdv0z+/Xb0QrPJSjau44=; b=msJpR1C0RI3RsmKFURTQbm1bdTNLUT0 uAVVtIORhaY8gMUmtSygSg2zPbRrQlf5zutBpcR7pv3pk+Qf93QTLvb3dTXVs29u Ko638oxhMRzcsxAxBeLb3r3XBeeZsB6QVqICRtEsiyRzzQsFGKaYvrsCNiutNWKN qG7gP2JtL7X8= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from pegasus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (pegasus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 8Crx2tVZZVAy for ; Wed, 22 Nov 2017 12:21:59 +0100 (CET) Received: from HTCAONE.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1 with cipher ECDHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTPS for ; Wed, 22 Nov 2017 12:21:59 +0100 (CET) Received: from localhost (141.80.180.135) by HTCAONE.mdc-berlin.net (141.80.180.125) with Microsoft SMTP Server (TLS) id 14.3.361.1; Wed, 22 Nov 2017 12:21:58 +0100 User-agent: mu4e 0.9.18; emacs 25.3.1 From: Ricardo Wurmus To: Subject: [PATCH 00/12] Add Java dependencies for FastQC X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Wed, 22 Nov 2017 12:21:58 +0100 Message-ID: <87zi7ev9rd.fsf@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.180.135] X-TM-AS-Product-Ver: SMEX-11.0.0.4283-8.100.1062-23482.005 X-TM-AS-Result: No--2.211500-0.000000-31 X-TM-AS-MatchedID: 703113-702039-703786-704421-702015-702143-862883-148004-1 48036-10019-41000-42000-42003-63 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] [fuzzy] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: submit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.0 (-----) The following patch series adds dependencies for the popular bioinfo tool FastQC. Ricardo Wurmus (12): gnu: Add java-snappy-1. gnu: Add javacc. gnu: Add javacc-4. gnu: Add java-commons-jexl-2. gnu: java-htsjdk: Update to 2.3.0. gnu: Add java-picard. gnu: Add java-cofoja. gnu: Add java-commons-bcel. gnu: Add ant-apache-bcel. gnu: Add ant-junit. gnu: Add java-picard-1.113. gnu: Add java-jbzip2. gnu/packages/bioinformatics.scm | 216 +++++++++++++++++++++++++++++++- gnu/packages/compression.scm | 98 +++++++++++++++ gnu/packages/java.scm | 268 ++++++++++++++++++++++++++++++++++++++++ 3 files changed, 576 insertions(+), 6 deletions(-) -- 2.14.1 From debbugs-submit-bounces@debbugs.gnu.org Wed Nov 22 06:31:02 2017 Received: (at 29394) by debbugs.gnu.org; 22 Nov 2017 11:31:02 +0000 Received: from localhost ([127.0.0.1]:51903 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1eHTF7-0007rS-Ly for submit@debbugs.gnu.org; Wed, 22 Nov 2017 06:31:01 -0500 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:35952) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1eHTF5-0007rJ-CI for 29394@debbugs.gnu.org; Wed, 22 Nov 2017 06:30:59 -0500 Received: from localhost (localhost [127.0.0.1]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 6269C38092A; Wed, 22 Nov 2017 12:30:58 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:x-mailer:message-id:date :date:subject:subject:from:from:received:received:received; s= mdc; t=1511350257; x=1513164658; bh=opkoS6jvYl1BcOlnQ+k3Y4/WKHUG cBCURQmQq5AzIZY=; b=Dhau9/qAvFPOoUdrJJ4kOzSLh8ckKzTxFwgPsUwWLyKV 0kudXoXrqG/sc/x8+WjQ3LL/KFmjVfbpABLQm/G2QSsyri4T906bfsHe6+MQGGiz 3/eOr4GKVHINbruxY37NLAm1Fv5OEOt1hJmr0kbJu+tzX6ul/d3lsMd6vvzQVvM= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from venus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (venus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id LwVH2Z5hgggx; Wed, 22 Nov 2017 12:30:57 +0100 (CET) Received: from HTCAONE.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1 with cipher ECDHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTPS; Wed, 22 Nov 2017 12:30:57 +0100 (CET) Received: from banana.mdc-berlin.net (141.80.180.135) by HTCAONE.mdc-berlin.net (141.80.180.125) with Microsoft SMTP Server (TLS) id 14.3.361.1; Wed, 22 Nov 2017 12:30:57 +0100 From: To: <29394@debbugs.gnu.org> Subject: [PATCH 01/12] gnu: Add java-snappy-1. Date: Wed, 22 Nov 2017 12:30:31 +0100 Message-ID: <20171122113042.1734-1-ricardo.wurmus@mdc-berlin.de> X-Mailer: git-send-email 2.15.0 MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.180.135] X-TM-AS-Product-Ver: SMEX-11.0.0.4283-8.100.1062-23482.005 X-TM-AS-Result: No--6.712000-0.000000-31 X-TM-AS-MatchedID: 700486-703786-704425-188019-704496-701590-706817-709251-1 39705-704852-706561-704421-106420-847575-700079-188198-706290-701719-105700 -704980-139504-706249-703176-700748-105250-705178-701407-700970-148004-1480 36-29997-42000-42003-63 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 29394 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.0 (-----) From: Ricardo Wurmus * gnu/packages/compression.scm (java-snappy-1): New variable. --- gnu/packages/compression.scm | 58 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 58 insertions(+) diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index 748c75a74..193d36797 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -1206,6 +1206,64 @@ install: libbitshuffle.so compresser/decompresser.") (license license:asl2.0))) +(define-public java-snappy-1 + (package + (inherit java-snappy) + (version "1.0.3-rc3") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/xerial/snappy-java/archive/" + "snappy-java-" version ".tar.gz")) + (sha256 + (base32 + "08hsxlqidiqck0q57fshwyv3ynyxy18vmhrai9fyc8mz17m7gsa3")))) + (arguments + `(#:jar-name "snappy.jar" + #:source-dir "src/main/java" + #:phases + (modify-phases %standard-phases + (add-before 'build 'remove-binaries + (lambda _ + (delete-file "lib/org/xerial/snappy/OSInfo.class") + (delete-file-recursively "src/main/resources/org/xerial/snappy/native") + #t)) + (add-before 'build 'build-jni + (lambda _ + ;; Rebuild one of the binaries we removed earlier + (system* "javac" "src/main/java/org/xerial/snappy/OSInfo.java" + "-d" "lib") + ;; Link to the dynamic snappy, not the static ones + (substitute* "Makefile.common" + (("-shared") "-shared -lsnappy")) + (substitute* "Makefile" + ;; Don't download the sources here. + (("\\$\\(SNAPPY_UNPACKED\\) ") "") + ((": \\$\\(SNAPPY_UNPACKED\\) ") ":") + ;; What we actually want to build + (("SNAPPY_OBJ:=.*") + "SNAPPY_OBJ:=$(addprefix $(SNAPPY_OUT)/, SnappyNative.o)\n") + ;; Since we removed the directory structure in "native" during + ;; the previous phase, we need to recreate it. + (("NAME\\): \\$\\(SNAPPY_OBJ\\)") + "NAME): $(SNAPPY_OBJ)\n\t@mkdir -p $(@D)")) + ;; Finally we can run the Makefile to build the dynamic library. + (zero? (system* "make" "native")))) + ;; Once we have built the shared library, we need to place it in the + ;; "build" directory so it can be added to the jar file. + (add-after 'build-jni 'copy-jni + (lambda _ + (copy-recursively "src/main/resources/org/xerial/snappy/native" + "build/classes/org/xerial/snappy/native") + #t)) + (add-before 'check 'fix-tests + (lambda _ + (mkdir-p "src/test/resources/org/xerial/snappy/") + (copy-recursively "src/test/java/org/xerial/snappy/testdata" + "src/test/resources/org/xerial/snappy/testdata") + (install-file "src/test/java/org/xerial/snappy/alice29.txt" + "src/test/resources/org/xerial/snappy/") + #t))))))) + (define-public java-iq80-snappy (package (name "java-iq80-snappy") -- 2.14.1 From debbugs-submit-bounces@debbugs.gnu.org Wed Nov 22 06:31:09 2017 Received: (at 29394) by debbugs.gnu.org; 22 Nov 2017 11:31:09 +0000 Received: from localhost ([127.0.0.1]:51906 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1eHTFF-0007s3-26 for submit@debbugs.gnu.org; Wed, 22 Nov 2017 06:31:09 -0500 Received: from sinope02.bbbm.mdc-berlin.de ([141.80.25.24]:40450) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1eHTFC-0007ru-FW for 29394@debbugs.gnu.org; Wed, 22 Nov 2017 06:31:07 -0500 Received: from localhost (localhost [127.0.0.1]) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTP id 6F3D2DB97D2; Wed, 22 Nov 2017 12:31:05 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:references:in-reply-to :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1511350259; x=1513164660; bh=z3Td1EUJkBm/hI1+xbN5vK7fhhwS5pnzrgaaKlSrZ8o=; b=J8/k5+fMwQZw FJcoxzz8P4oo4mbQ2/KexO+d7zHVt9IqhFW0F16RW4vj+w3vzGsCUUGGmoUa9srJ UDS5CZww9Hq6KlBOnizIB3vEgj0XrVFWnJZCQR9TMZ8qVUuvzGA23OcAwXzkZfti 33niID2CqBt2g40Y8M4pyyDFKx+/R7o= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from sinope02.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope02.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id zfEnLJXOO52C; Wed, 22 Nov 2017 12:30:59 +0100 (CET) Received: from HTCAONE.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1 with cipher ECDHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTPS; Wed, 22 Nov 2017 12:30:58 +0100 (CET) Received: from banana.mdc-berlin.net (141.80.180.135) by HTCAONE.mdc-berlin.net (141.80.180.125) with Microsoft SMTP Server (TLS) id 14.3.361.1; Wed, 22 Nov 2017 12:30:58 +0100 From: To: <29394@debbugs.gnu.org> Subject: [PATCH 02/12] gnu: Add javacc. Date: Wed, 22 Nov 2017 12:30:32 +0100 Message-ID: <20171122113042.1734-2-ricardo.wurmus@mdc-berlin.de> X-Mailer: git-send-email 2.15.0 In-Reply-To: <20171122113042.1734-1-ricardo.wurmus@mdc-berlin.de> References: <20171122113042.1734-1-ricardo.wurmus@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.180.135] X-TM-AS-Product-Ver: SMEX-11.0.0.4283-8.100.1062-23482.005 X-TM-AS-Result: No--5.524900-0.000000-31 X-TM-AS-MatchedID: 700486-703786-704425-188019-704496-701590-706817-709251-1 39705-700970-706561-704421-847575-704568-703113-702358-702039-701559-862934 -708752-148004-148036-42000-42003-63 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 29394 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.0 (/) From: Ricardo Wurmus * gnu/packages/java.scm (javacc): New variable. --- gnu/packages/java.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index bd6c00365..eae4aa750 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -1893,6 +1893,38 @@ designs.") license:asl2.0 license:cpl1.0))))) +(define-public javacc + (package + (name "javacc") + (version "7.0.3") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/javacc/javacc/" + "archive/" version ".tar.gz")) + (file-name (string-append "javacc-" version ".tar.gz")) + (sha256 + (base32 + "111xc9mnmc5a6qz6x3xbhqc07y1lg2b996ggzw0hrblg42zya9xf")))) + (build-system ant-build-system) + (arguments + `(#:test-target "test" + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'delete-bundled-libs + (lambda _ + (delete-file-recursively "lib") #t)) + (replace 'install (install-jars "target"))))) + (home-page "https://javacc.org/") + (synopsis "Java parser generator") + (description "Java Compiler Compiler (JavaCC) is the most popular parser +generator for use with Java applications. A parser generator is a tool that +reads a grammar specification and converts it to a Java program that can +recognize matches to the grammar. In addition to the parser generator itself, +JavaCC provides other standard capabilities related to parser generation such +as tree building (via a tool called JJTree included with JavaCC), actions, +debugging, etc.") + (license license:bsd-3))) + (define-public java-classpathx-servletapi (package (name "java-classpathx-servletapi") -- 2.14.1 From debbugs-submit-bounces@debbugs.gnu.org Wed Nov 22 06:31:29 2017 Received: (at 29394) by debbugs.gnu.org; 22 Nov 2017 11:31:29 +0000 Received: from localhost ([127.0.0.1]:51909 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1eHTFZ-0007sg-Be for submit@debbugs.gnu.org; Wed, 22 Nov 2017 06:31:29 -0500 Received: from sinope02.bbbm.mdc-berlin.de ([141.80.25.24]:40492) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1eHTFX-0007sX-Qh for 29394@debbugs.gnu.org; Wed, 22 Nov 2017 06:31:28 -0500 Received: from localhost (localhost [127.0.0.1]) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTP id 24328DB97F3; Wed, 22 Nov 2017 12:31:27 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:references:in-reply-to :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1511350281; x=1513164682; bh=+d9PXcku9rB1gLOSU0Ig8YTeTMReNLGr9iQMi+ayh7w=; b=iwcWFqU+9smh KSMf2XmNLD6du/GQUpym9JpyvCsXVe4xaxMkxStUaNnlvnb8c+gRg8GkBSHBQN5W MxkBrT/2pj5BrrKM0B/WshZOYZj6v97T+86j1U5Jd5CajCp2nM527GHiFhav8Mji MMCr7az6tt3Gb9Wyi38YdyRk21hxWow= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from sinope02.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope02.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id s3gQ9YO8v0Nj; Wed, 22 Nov 2017 12:31:21 +0100 (CET) Received: from HTCAONE.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1 with cipher ECDHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTPS; Wed, 22 Nov 2017 12:31:21 +0100 (CET) Received: from banana.mdc-berlin.net (141.80.180.135) by HTCAONE.mdc-berlin.net (141.80.180.125) with Microsoft SMTP Server (TLS) id 14.3.361.1; Wed, 22 Nov 2017 12:31:05 +0100 From: To: <29394@debbugs.gnu.org> Subject: [PATCH 03/12] gnu: Add javacc-4. Date: Wed, 22 Nov 2017 12:30:33 +0100 Message-ID: <20171122113042.1734-3-ricardo.wurmus@mdc-berlin.de> X-Mailer: git-send-email 2.15.0 In-Reply-To: <20171122113042.1734-1-ricardo.wurmus@mdc-berlin.de> References: <20171122113042.1734-1-ricardo.wurmus@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.180.135] X-TM-AS-Product-Ver: SMEX-11.0.0.4283-8.100.1062-23482.005 X-TM-AS-Result: No--3.440100-0.000000-31 X-TM-AS-MatchedID: 700486-703786-704425-188019-702039-708752-704496-701590-7 06817-139705-709251-701407-700970-706561-704421-847575-148004-148036-42000- 42003-63 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 29394 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.0 (/) From: Ricardo Wurmus * gnu/packages/java.scm (javacc-4): New variable. --- gnu/packages/java.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index eae4aa750..2691f2f39 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -1925,6 +1925,30 @@ as tree building (via a tool called JJTree included with JavaCC), actions, debugging, etc.") (license license:bsd-3))) +(define-public javacc-4 + (package (inherit javacc) + (version "4.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/javacc/javacc.git") + (commit "release_41"))) + (file-name (string-append "javacc-" version "-checkout")) + (sha256 + (base32 + "07ysav7j8r1c6h8qxrgqk6lwdp74ly0ad1935lragxml0qqc3ka0")))) + ;; Tests fail with + ;; /tmp/guix-build-javacc-4.1.drv-0/source/test/javacodeLA/build.xml:60: + ;; JAVACODE failed + (arguments + `(#:tests? #f + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'delete-bundled-libs + (lambda _ + (delete-file-recursively "lib") #t)) + (replace 'install (install-jars "bin/lib"))))))) + (define-public java-classpathx-servletapi (package (name "java-classpathx-servletapi") -- 2.14.1 From debbugs-submit-bounces@debbugs.gnu.org Wed Nov 22 06:31:51 2017 Received: (at 29394) by debbugs.gnu.org; 22 Nov 2017 11:31:52 +0000 Received: from localhost ([127.0.0.1]:51912 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1eHTFv-0007tL-Kz for submit@debbugs.gnu.org; Wed, 22 Nov 2017 06:31:51 -0500 Received: from sinope02.bbbm.mdc-berlin.de ([141.80.25.24]:40528) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1eHTFu-0007tD-0X for 29394@debbugs.gnu.org; Wed, 22 Nov 2017 06:31:50 -0500 Received: from localhost (localhost [127.0.0.1]) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTP id 47EC4DB981B; Wed, 22 Nov 2017 12:31:49 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:references:in-reply-to :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1511350304; x=1513164705; bh=kbUkb60BTxZZa12ObJ5Eq6hrIeqm7tscbBYDXAStZXE=; b=SRn4bDCUKB4C Qs/26nMi0ELi9p/NeLJFWDP+pgeXbmeLDZSFYIgl6QLcYV8tCmdxvBBMJgSkGAro sqou03wk9qvTSf2DIddBplKINnJGHWhZQKuAo84G4rX0HKMllKqyocyYBhE85C9d XvyHc3P+zMM7hLwdoOtmhiFfSq1u8B4= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from sinope02.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope02.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id BsamRv-cU5fO; Wed, 22 Nov 2017 12:31:44 +0100 (CET) Received: from HTCAONE.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1 with cipher ECDHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTPS; Wed, 22 Nov 2017 12:31:44 +0100 (CET) Received: from banana.mdc-berlin.net (141.80.180.135) by HTCAONE.mdc-berlin.net (141.80.180.125) with Microsoft SMTP Server (TLS) id 14.3.361.1; Wed, 22 Nov 2017 12:31:27 +0100 From: To: <29394@debbugs.gnu.org> Subject: [PATCH 04/12] gnu: Add java-commons-jexl-2. Date: Wed, 22 Nov 2017 12:30:34 +0100 Message-ID: <20171122113042.1734-4-ricardo.wurmus@mdc-berlin.de> X-Mailer: git-send-email 2.15.0 In-Reply-To: <20171122113042.1734-1-ricardo.wurmus@mdc-berlin.de> References: <20171122113042.1734-1-ricardo.wurmus@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.180.135] X-TM-AS-Product-Ver: SMEX-11.0.0.4283-8.100.1062-23482.005 X-TM-AS-Result: No--0.957800-0.000000-31 X-TM-AS-MatchedID: 700486-703786-702015-704425-188019-700537-707788-709251-7 04496-701590-706817-700808-704852-706561-704421-105250-704983-701407-188198 -702106-105040-700970-706725-847575-701461-709908-702169-700756-706249-7013 84-121618-136070-703176-139705-704568-863828-706427-701132-701848-148004-14 8036-29997-42000-42003-63 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 29394 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.0 (/) From: Ricardo Wurmus * gnu/packages/java.scm (java-commons-jexl-2): New variable. --- gnu/packages/java.scm | 57 +++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 57 insertions(+) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 2691f2f39..f78f63c72 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -6991,6 +6991,63 @@ In addition to the expression language, MVEL serves as a templating language for configuration and string construction.") (license license:asl2.0))) +(define-public java-commons-jexl-2 + (package + (name "java-commons-jexl") + (version "2.1.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://apache/commons/jexl/source/" + "commons-jexl-" version "-src.tar.gz")) + (sha256 + (base32 + "1ai7632bwwaxglb0nbpblpr2jw5g20afrsaq372ipkphi3ncy1jz")))) + (build-system ant-build-system) + (arguments + `(#:jar-name "commons-jexl-2.jar" + #:jdk ,icedtea-8 + #:source-dir "src/main/java" + #:phases + (modify-phases %standard-phases + (add-before 'check 'disable-broken-tests + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "src/test/java/org/apache/commons/jexl2/" + (substitute* "ArithmeticTest.java" + (("asserter.assertExpression\\(\"3 / 0\"") "//") + (("asserter.assertExpression\\(\"imanull") "//")) + ;; This test fails with "ambiguous method invocation" + (delete-file "CacheTest.java") + ;; This test doesn't have access to the temp directory + (substitute* "ClassCreatorTest.java" + (("java.io.tmpdir") "user.dir")) + ;; This test fails in trying to detect whether it can run. + (substitute* "ClassCreator.java" + (("boolean canRun =.*") "boolean canRun = false;\n")) + ;; ...and these tests depend on it. + (delete-file "scripting/JexlScriptEngineOptionalTest.java") + (delete-file "scripting/JexlScriptEngineTest.java")) + #t)) + (add-before 'build 'run-javacc + (lambda _ + (with-directory-excursion "src/main/java/org/apache/commons/jexl2/parser/" + (and (zero? (system* "java" "jjtree" "Parser.jjt")) + (zero? (system* "java" "javacc" "Parser.jj"))))))))) + (inputs + `(("java-commons-logging-minimal" ,java-commons-logging-minimal))) + (native-inputs + `(("java-junit" ,java-junit) + ("java-hamcrest-core" ,java-hamcrest-core) + ("javacc" ,javacc-4))) + (home-page "https://commons.apache.org/proper/commons-jexl/") + (synopsis "Java Expression Language ") + (description "JEXL is a library intended to facilitate the implementation +of dynamic and scripting features in applications and frameworks written in +Java. JEXL implements an Expression Language based on some extensions to the +JSTL Expression Language supporting most of the constructs seen in +shell-script or ECMAScript. Its goal is to expose scripting features usable +by technical operatives or consultants working with enterprise platforms.") + (license license:asl2.0))) + (define-public java-lz4 (package (name "java-lz4") -- 2.14.1 From debbugs-submit-bounces@debbugs.gnu.org Wed Nov 22 06:32:45 2017 Received: (at 29394) by debbugs.gnu.org; 22 Nov 2017 11:32:45 +0000 Received: from localhost ([127.0.0.1]:51919 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1eHTGm-0007v9-0l for submit@debbugs.gnu.org; Wed, 22 Nov 2017 06:32:45 -0500 Received: from sinope02.bbbm.mdc-berlin.de ([141.80.25.24]:40584) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1eHTGk-0007v0-82 for 29394@debbugs.gnu.org; Wed, 22 Nov 2017 06:32:42 -0500 Received: from localhost (localhost [127.0.0.1]) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTP id B285FDB9854; Wed, 22 Nov 2017 12:32:41 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:references:in-reply-to :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1511350356; x=1513164757; bh=KXojxIufBgFoJvS/8OPeQO4OyxoKIyqc8sZfcf9yOA0=; b=tkoahHZDyToa mAogLyyzPeDffcdNFvpv2+Ya0+wufo+PoD1m/KwMCkJWcsaH4hyS2bporp74dgL8 3s4W8o/46vlMKvK86S14J8LE/W8zZpn513GwLXWQ6kXbDCaKpvvWrZgHu9bavZp7 s4LB8MTz9+9Wfw8Hn60XIbUpm0Q6HuY= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from sinope02.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope02.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id gRYxOA0za3-T; Wed, 22 Nov 2017 12:32:36 +0100 (CET) Received: from HTCAONE.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1 with cipher ECDHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTPS; Wed, 22 Nov 2017 12:32:36 +0100 (CET) Received: from banana.mdc-berlin.net (141.80.180.135) by HTCAONE.mdc-berlin.net (141.80.180.125) with Microsoft SMTP Server (TLS) id 14.3.361.1; Wed, 22 Nov 2017 12:31:49 +0100 From: To: <29394@debbugs.gnu.org> Subject: [PATCH 05/12] gnu: java-htsjdk: Update to 2.3.0. Date: Wed, 22 Nov 2017 12:30:35 +0100 Message-ID: <20171122113042.1734-5-ricardo.wurmus@mdc-berlin.de> X-Mailer: git-send-email 2.15.0 In-Reply-To: <20171122113042.1734-1-ricardo.wurmus@mdc-berlin.de> References: <20171122113042.1734-1-ricardo.wurmus@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.180.135] X-TM-AS-Product-Ver: SMEX-11.0.0.4283-8.100.1062-23482.005 X-TM-AS-Result: No--6.574600-0.000000-31 X-TM-AS-MatchedID: 700486-703786-702143-704421-702015-188019-704496-701590-7 06817-709251-701762-106420-188198-701384-847575-701407-700970-710442-709908 -706561-101030-701632-704568-148004-148036-42000-42003-63 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 29394 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.0 (/) From: Ricardo Wurmus * gnu/packages/bioinformatics.scm (java-htsjdk): Update to 2.3.0. [arguments]: Build with JDK 8. [inputs]: Add java-ngs, java-snappy, java-commons-compress, java-commons-logging-minimal, java-commons-jexl-2, and java-xz. [native-inputs]: Add java-testng. --- gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++------ 1 file changed, 18 insertions(+), 6 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a8d7361ff..6c71d7362 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2961,7 +2961,7 @@ from high-throughput sequencing assays.") (define-public java-htsjdk (package (name "java-htsjdk") - (version "1.129") + (version "2.3.0") ; last version without build dependency on gradle (source (origin (method url-fetch) (uri (string-append @@ -2970,15 +2970,18 @@ from high-throughput sequencing assays.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0asdk9b8jx2ij7yd6apg9qx03li8q7z3ml0qy2r2qczkra79y6fw")) + "1ibhzzxsfc38nqyk9r8zqj6blfc1kh26iirypd4q6n90hs2m6nyq")) (modules '((guix build utils))) - ;; remove build dependency on git - (snippet '(substitute* "build.xml" - (("failifexecutionfails=\"true\"") - "failifexecutionfails=\"false\""))))) + (snippet + ;; Delete pre-built binaries + '(begin + (delete-file-recursively "lib") + (mkdir-p "lib") + #t)))) (build-system ant-build-system) (arguments `(#:tests? #f ; test require Internet access + #:jdk ,icedtea-8 #:make-flags (list (string-append "-Ddist=" (assoc-ref %outputs "out") "/share/java/htsjdk/")) @@ -2987,6 +2990,15 @@ from high-throughput sequencing assays.") (modify-phases %standard-phases ;; The build phase also installs the jars (delete 'install)))) + (inputs + `(("java-ngs" ,java-ngs) + ("java-snappy-1" ,java-snappy-1) + ("java-commons-compress" ,java-commons-compress) + ("java-commons-logging-minimal" ,java-commons-logging-minimal) + ("java-commons-jexl-2" ,java-commons-jexl-2) + ("java-xz" ,java-xz))) + (native-inputs + `(("java-testng" ,java-testng))) (home-page "http://samtools.github.io/htsjdk/") (synopsis "Java API for high-throughput sequencing data (HTS) formats") (description -- 2.14.1 From debbugs-submit-bounces@debbugs.gnu.org Wed Nov 22 06:33:27 2017 Received: (at 29394) by debbugs.gnu.org; 22 Nov 2017 11:33:27 +0000 Received: from localhost ([127.0.0.1]:51923 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1eHTHS-0007wV-PS for submit@debbugs.gnu.org; Wed, 22 Nov 2017 06:33:27 -0500 Received: from sinope02.bbbm.mdc-berlin.de ([141.80.25.24]:40702) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1eHTHR-0007wN-9q for 29394@debbugs.gnu.org; Wed, 22 Nov 2017 06:33:25 -0500 Received: from localhost (localhost [127.0.0.1]) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTP id BF4B4DB98B7; Wed, 22 Nov 2017 12:33:24 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:references:in-reply-to :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1511350399; x=1513164800; bh=uU6/12jT5GOHk9AFkEc6C2GMqkQJwNhLXOK926D0ycw=; b=b1zaYb4WCx5K EBrBMvlt5YiJ3ezmCIkm9poi4AY6nmbdwPyR54H8GFKg8Li9nt1UQvLv39XAqfZg 7vnDkjWX366WnDVVO8XMmPQmuwcaw/qU5130lsM0rch2V9T/vFkfpSdIHQrWHCxp CFKd14rmh7BjfsRa4UiggHmn+1v72XM= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from sinope02.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope02.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 6j_IKNA94Jvk; Wed, 22 Nov 2017 12:33:19 +0100 (CET) Received: from HTCAONE.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1 with cipher ECDHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTPS; Wed, 22 Nov 2017 12:33:19 +0100 (CET) Received: from banana.mdc-berlin.net (141.80.180.135) by HTCAONE.mdc-berlin.net (141.80.180.125) with Microsoft SMTP Server (TLS) id 14.3.361.1; Wed, 22 Nov 2017 12:32:22 +0100 From: To: <29394@debbugs.gnu.org> Subject: [PATCH 06/12] gnu: Add java-picard. Date: Wed, 22 Nov 2017 12:30:36 +0100 Message-ID: <20171122113042.1734-6-ricardo.wurmus@mdc-berlin.de> X-Mailer: git-send-email 2.15.0 In-Reply-To: <20171122113042.1734-1-ricardo.wurmus@mdc-berlin.de> References: <20171122113042.1734-1-ricardo.wurmus@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.180.135] X-TM-AS-Product-Ver: SMEX-11.0.0.4283-8.100.1062-23482.005 X-TM-AS-Result: No--1.226000-0.000000-31 X-TM-AS-MatchedID: 700486-703786-704425-188019-709584-701594-701559-710442-7 04496-701590-706817-139705-709251-701762-847575-188198-106420-701384-702358 -700752-701407-700970-700748-706803-706561-704421-702106-105040-101030-7016 32-704568-707451-702376-139630-148004-148036-29997-42000-42003-63 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 29394 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.0 (/) From: Ricardo Wurmus * gnu/packages/bioinformatics.scm (java-picard): New variable. --- gnu/packages/bioinformatics.scm | 78 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 78 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6c71d7362..0896edf25 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3008,6 +3008,84 @@ sequencing (HTS) data. There are also an number of useful utilities for manipulating HTS data.") (license license:expat))) +;; This version matches java-htsjdk 2.3.0. Later versions also require a more +;; recent version of java-htsjdk, which depends on gradle. +(define-public java-picard + (package + (name "java-picard") + (version "2.3.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/broadinstitute/picard.git") + (commit version))) + (file-name (string-append "java-picard-" version "-checkout")) + (sha256 + (base32 + "1ll7mf4r3by92w2nhlmpa591xd1f46xlkwh59mq6fvbb5pdwzvx6")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Delete pre-built binaries. + (delete-file-recursively "lib") + (mkdir-p "lib") + (substitute* "build.xml" + ;; Remove build-time dependency on git. + (("failifexecutionfails=\"true\"") + "failifexecutionfails=\"false\"") + ;; Use our htsjdk. + (("depends=\"compile-htsjdk, ") + "depends=\"") + (("depends=\"compile-htsjdk-tests, ") + "depends=\"") + ;; Build picard-lib.jar before building picard.jar + (("name=\"picard-jar\" depends=\"" line) + (string-append line "picard-lib-jar, "))) + #t)))) + (build-system ant-build-system) + (arguments + `(#:build-target "picard-jar" + #:test-target "test" + ;; Tests require jacoco:coverage. + #:tests? #f + #:make-flags + (list (string-append "-Dhtsjdk_lib_dir=" + (assoc-ref %build-inputs "java-htsjdk") + "/share/java/htsjdk/") + "-Dhtsjdk-classes=dist/tmp" + (string-append "-Dhtsjdk-version=" + ,(package-version java-htsjdk))) + #:jdk ,icedtea-8 + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-our-htsjdk + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "build.xml" + (("\\$\\{htsjdk\\}/lib") + (string-append (assoc-ref inputs "java-htsjdk") + "/share/java/htsjdk/"))) + #t)) + (add-after 'unpack 'make-test-target-independent + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "build.xml" + (("name=\"test\" depends=\"compile, ") + "name=\"test\" depends=\"")) + #t)) + (replace 'install (install-jars "dist"))))) + (inputs + `(("java-htsjdk" ,java-htsjdk) + ("java-guava" ,java-guava))) + (native-inputs + `(("java-testng" ,java-testng))) + (home-page "http://broadinstitute.github.io/picard/") + (synopsis "Tools for manipulating high-throughput sequencing data and formats") + (description "Picard is a set of Java command line tools for manipulating +high-throughput sequencing (HTS) data and formats. Picard is implemented +using the HTSJDK Java library to support accessing file formats that are +commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and +VCF.") + (license license:expat))) + (define-public htslib (package (name "htslib") -- 2.14.1 From debbugs-submit-bounces@debbugs.gnu.org Wed Nov 22 06:33:46 2017 Received: (at 29394) by debbugs.gnu.org; 22 Nov 2017 11:33:46 +0000 Received: from localhost ([127.0.0.1]:51926 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1eHTHm-0007x4-8F for submit@debbugs.gnu.org; Wed, 22 Nov 2017 06:33:46 -0500 Received: from sinope02.bbbm.mdc-berlin.de ([141.80.25.24]:40744) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1eHTHi-0007wr-FC for 29394@debbugs.gnu.org; Wed, 22 Nov 2017 06:33:42 -0500 Received: from localhost (localhost [127.0.0.1]) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTP id E7A68DB98DD; Wed, 22 Nov 2017 12:33:41 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:references:in-reply-to :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1511350416; x=1513164817; bh=x1O9sISO57qCEMtoDmscHQGGrviqokXR2B/7Sv6uZTY=; b=VgPbaHUAc0// L2kkxiSxC5DtoSYLvWqeHORWZnQWvV6QLDuZIfS6VwGJ6HeiBG6C4wyz8Lbkk/O4 xxNDPMxLWV/9jEVZ31dDuHAJOeXUmBiHR9B4WTwr4qFS94lmPECZQfaKPWtoSS2m DexdRAwz7IqOFzyEjP1/umZna1wIvs8= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from sinope02.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope02.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id PXGLsn2X--n6; Wed, 22 Nov 2017 12:33:36 +0100 (CET) Received: from HTCAONE.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1 with cipher ECDHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTPS; Wed, 22 Nov 2017 12:33:36 +0100 (CET) Received: from banana.mdc-berlin.net (141.80.180.135) by HTCAONE.mdc-berlin.net (141.80.180.125) with Microsoft SMTP Server (TLS) id 14.3.361.1; Wed, 22 Nov 2017 12:32:52 +0100 From: To: <29394@debbugs.gnu.org> Subject: [PATCH 07/12] gnu: Add java-cofoja. Date: Wed, 22 Nov 2017 12:30:37 +0100 Message-ID: <20171122113042.1734-7-ricardo.wurmus@mdc-berlin.de> X-Mailer: git-send-email 2.15.0 In-Reply-To: <20171122113042.1734-1-ricardo.wurmus@mdc-berlin.de> References: <20171122113042.1734-1-ricardo.wurmus@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.180.135] X-TM-AS-Product-Ver: SMEX-11.0.0.4283-8.100.1062-23482.005 X-TM-AS-Result: No--8.596500-0.000000-31 X-TM-AS-MatchedID: 700486-703786-704425-188019-700782-863174-704496-701590-7 06817-139705-709251-706803-700970-701762-706561-700079-705927-704421-188198 -702106-105040-300015-710739-862883-704568-702626-702039-707997-706249-7070 27-706290-148004-148036-42000-42003-63 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 29394 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.0 (/) From: Ricardo Wurmus * gnu/packages/java.scm (java-cofoja): New variable. --- gnu/packages/java.scm | 56 +++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 56 insertions(+) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index f78f63c72..0cc9adf19 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -6515,6 +6515,62 @@ provides control over value quantization behavior across the value range and the subsequent value resolution at any given level.") (license license:public-domain))) +(define-public java-cofoja + (package + (name "java-cofoja") + (version "1.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/nhatminhle/cofoja.git") + (commit (string-append "v" version)))) + (file-name (string-append "java-cofoja-" version "-checkout")) + (sha256 + (base32 + "0p7sz8y5xgpi5rx1qwn6587fkd52qr3ha3ybh14gqcyxhikl525w")))) + (build-system ant-build-system) + (arguments + `(#:build-target "dist" + #:test-target "test" + #:jdk ,icedtea-8 + #:make-flags + (list "-Ddist.dir=dist") + #:modules ((guix build ant-build-system) + (guix build java-utils) + (guix build utils) + (srfi srfi-1) + (ice-9 match)) + #:phases + (modify-phases %standard-phases + ;; The bulid system ignores the class path the ant-build-system sets + ;; up and instead expects to find all dependencies in the "lib" + ;; directory. + (add-after 'unpack 'create-libdir + (lambda* (#:key inputs #:allow-other-keys) + (mkdir-p "lib") + (for-each + (lambda (file) + (let ((target (string-append "lib/" (basename file)))) + (unless (file-exists? target) + (symlink file target)))) + (append-map (match-lambda + ((label . dir) + (find-files dir "\\.jar$"))) + inputs)) + #t)) + (replace 'install (install-jars "dist"))))) + (inputs + `(("java-asm" ,java-asm))) + (native-inputs + `(("java-junit" ,java-junit))) + (home-page "https://github.com/nhatminhle/cofoja") + (synopsis "Contracts for Java") + (description "Contracts for Java, or Cofoja for short, is a contract +programming framework and test tool for Java, which uses annotation processing +and bytecode instrumentation to provide run-time checking. (In particular, +this is not a static analysis tool.)") + (license license:lgpl3+))) + (define-public java-aopalliance (package (name "java-aopalliance") -- 2.14.1 From debbugs-submit-bounces@debbugs.gnu.org Wed Nov 22 06:34:00 2017 Received: (at 29394) by debbugs.gnu.org; 22 Nov 2017 11:34:00 +0000 Received: from localhost ([127.0.0.1]:51929 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1eHTI0-0007xW-Hh for submit@debbugs.gnu.org; Wed, 22 Nov 2017 06:34:00 -0500 Received: from sinope02.bbbm.mdc-berlin.de ([141.80.25.24]:40790) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1eHTHy-0007xO-B4 for 29394@debbugs.gnu.org; Wed, 22 Nov 2017 06:33:58 -0500 Received: from localhost (localhost [127.0.0.1]) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTP id C87B8DB98F6; Wed, 22 Nov 2017 12:33:57 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:references:in-reply-to :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1511350432; x=1513164833; bh=eRXey/iS/HjZ113b4DlXaMgI5KgWgafWqriTrHykqLk=; b=U1OEOiFMFnXY LEzO5P6VijNHS3+FzgKqKybt+Ra3WuhvkMmSA6NL01UIpJucDQPKfvMgsLP8dp6P vH9vs65z47B5pr2czlU7VUgAzFlhCGkOPgqpFslrkBTggm9cBWgy4bjmQLPlI7ST zHNG362fBXbfFZqkgB4lGY9A9FUrR+Q= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from sinope02.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope02.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id J682bbbTjOzA; Wed, 22 Nov 2017 12:33:52 +0100 (CET) Received: from HTCAONE.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1 with cipher ECDHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTPS; Wed, 22 Nov 2017 12:33:52 +0100 (CET) Received: from banana.mdc-berlin.net (141.80.180.135) by HTCAONE.mdc-berlin.net (141.80.180.125) with Microsoft SMTP Server (TLS) id 14.3.361.1; Wed, 22 Nov 2017 12:33:27 +0100 From: To: <29394@debbugs.gnu.org> Subject: [PATCH 08/12] gnu: Add java-commons-bcel. Date: Wed, 22 Nov 2017 12:30:38 +0100 Message-ID: <20171122113042.1734-8-ricardo.wurmus@mdc-berlin.de> X-Mailer: git-send-email 2.15.0 In-Reply-To: <20171122113042.1734-1-ricardo.wurmus@mdc-berlin.de> References: <20171122113042.1734-1-ricardo.wurmus@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.180.135] X-TM-AS-Product-Ver: SMEX-11.0.0.4283-8.100.1062-23482.005 X-TM-AS-Result: No--0.935700-0.000000-31 X-TM-AS-MatchedID: 700486-703786-702015-704425-188019-700476-704496-701590-7 06817-709251-700808-704852-700970-701407-710442-139705-701604-701014-704568 -702836-700079-862883-700748-704927-710224-709253-707911-712032-706249-7077 60-861157-702791-148004-148036-42000-42003-63 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 29394 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.0 (/) From: Ricardo Wurmus * gnu/packages/java.scm (java-commons-bcel): New variable. --- gnu/packages/java.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 0cc9adf19..d37a76aef 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -7235,6 +7235,41 @@ for high performance inter-thread communication that avoids the need for message queues or resource locking.") (license license:asl2.0))) +(define-public java-commons-bcel + (package + (name "java-commons-bcel") + (version "6.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://apache/commons/bcel/source/bcel-" + version "-src.tar.gz")) + (sha256 + (base32 + "0j3x1rxd673k07psclk8k13rqh0x0mf2yy5qiwkiw4z3afa568jy")))) + (build-system ant-build-system) + (arguments + `(#:jar-name "bcel.jar" + #:jdk ,icedtea-8 + #:source-dir "src/main/java" + #:test-dir "src/test/java" + ;; FIXME: Tests require the unpackaged jna. + #:tests? #f)) + (home-page "https://commons.apache.org/proper/commons-bcel/") + (synopsis "Byte code engineering library") + (description "The Byte Code Engineering Library (Apache Commons BCEL) is +intended to give users a convenient way to analyze, create, and +manipulate (binary) Java class files. Classes are represented by objects +which contain all the symbolic information of the given class: methods, fields +and byte code instructions, in particular. + +Such objects can be read from an existing file, be transformed by a +program (e.g. a class loader at run-time) and written to a file again. An +even more interesting application is the creation of classes from scratch at +run-time. The @dfn{Byte Code Engineering Library} (BCEL) may be also useful +if you want to learn about the @dfn{Java Virtual Machine} (JVM) and the format +of Java @code{.class} files.") + (license license:asl2.0))) + (define-public java-xerial-core (package (name "java-xerial-core") -- 2.14.1 From debbugs-submit-bounces@debbugs.gnu.org Wed Nov 22 06:34:41 2017 Received: (at 29394) by debbugs.gnu.org; 22 Nov 2017 11:34:41 +0000 Received: from localhost ([127.0.0.1]:51935 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1eHTIe-0007z5-Rp for submit@debbugs.gnu.org; Wed, 22 Nov 2017 06:34:41 -0500 Received: from sinope02.bbbm.mdc-berlin.de ([141.80.25.24]:40850) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1eHTIc-0007yx-UN for 29394@debbugs.gnu.org; Wed, 22 Nov 2017 06:34:39 -0500 Received: from localhost (localhost [127.0.0.1]) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTP id 660F0DB991F; Wed, 22 Nov 2017 12:34:38 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:references:in-reply-to :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1511350473; x=1513164874; bh=cJCfsgGwv6uKOKouO/1Ltz2mLHdWRhCHxeSTtHJ6wzE=; b=g+EOXlvriRzw k6bZtMDnHCxZxz70BqblJWG+s5n0t/eCF4SYx3Zi52K8484e+Yuuav6k7rqUo0fK Fn7OPx54STAeAajHHjAk0nDfamhc89Vu91FEGH9EGaUszN9ah8eeKQOBGtIF5+x+ nalAt3MIOpnkdNIhmjN7+FD0QTDFl1o= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from sinope02.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope02.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id ZIAGXzh64lYH; Wed, 22 Nov 2017 12:34:33 +0100 (CET) Received: from HTCAONE.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1 with cipher ECDHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTPS; Wed, 22 Nov 2017 12:34:33 +0100 (CET) Received: from banana.mdc-berlin.net (141.80.180.135) by HTCAONE.mdc-berlin.net (141.80.180.125) with Microsoft SMTP Server (TLS) id 14.3.361.1; Wed, 22 Nov 2017 12:33:57 +0100 From: To: <29394@debbugs.gnu.org> Subject: [PATCH 09/12] gnu: Add ant-apache-bcel. Date: Wed, 22 Nov 2017 12:30:39 +0100 Message-ID: <20171122113042.1734-9-ricardo.wurmus@mdc-berlin.de> X-Mailer: git-send-email 2.15.0 In-Reply-To: <20171122113042.1734-1-ricardo.wurmus@mdc-berlin.de> References: <20171122113042.1734-1-ricardo.wurmus@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.180.135] X-TM-AS-Product-Ver: SMEX-11.0.0.4283-8.100.1062-23482.005 X-TM-AS-Result: No--1.791500-0.000000-31 X-TM-AS-MatchedID: 700486-703786-704425-188019-700502-704421-188198-702106-1 05040-300015-709251-703720-862883-702015-847575-106420-148004-148036-29997- 42000-42003-63 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 29394 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.0 (/) From: Ricardo Wurmus * gnu/packages/java.scm (ant-apache-bcel): New variable. --- gnu/packages/java.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index d37a76aef..eca23d9da 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -1752,6 +1752,38 @@ IcedTea build harness.") (native-inputs `(("jdk" ,icedtea-7 "jdk"))))) +(define-public ant-apache-bcel + (package + (inherit ant/java8) + (name "ant-apache-bcel") + (arguments + (substitute-keyword-arguments (package-arguments ant/java8) + ((#:phases phases) + `(modify-phases ,phases + (add-after 'unpack 'link-bcel + (lambda* (#:key inputs #:allow-other-keys) + (for-each (lambda (file) + (symlink file + (string-append "lib/optional/" + (basename file)))) + (find-files (assoc-ref inputs "java-commons-bcel") + "\\.jar$")) + #t)) + (add-after 'build 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (share (string-append out "/share/java")) + (bin (string-append out "/bin")) + (lib (string-append out "/lib"))) + (mkdir-p share) + (install-file (string-append lib "/ant-apache-bcel.jar") share) + (delete-file-recursively bin) + (delete-file-recursively lib) + #t))))))) + (inputs + `(("java-commons-bcel" ,java-commons-bcel) + ,@(package-inputs ant/java8))))) + (define-public clojure (let* ((remove-archives '(begin (for-each delete-file -- 2.14.1 From debbugs-submit-bounces@debbugs.gnu.org Wed Nov 22 06:34:48 2017 Received: (at 29394) by debbugs.gnu.org; 22 Nov 2017 11:34:48 +0000 Received: from localhost ([127.0.0.1]:51939 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1eHTIm-0007zQ-3H for submit@debbugs.gnu.org; Wed, 22 Nov 2017 06:34:48 -0500 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:36072) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1eHTIk-0007zI-Pm for 29394@debbugs.gnu.org; Wed, 22 Nov 2017 06:34:47 -0500 Received: from localhost (localhost [127.0.0.1]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 377B73805AC; Wed, 22 Nov 2017 12:34:46 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:references:in-reply-to :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1511350485; x=1513164886; bh=KEUvMA+HEAsNafjjNFuz++vvplyzpyOsab/wtPU0Jz4=; b=SqRfHicwcz92 NDQOYoX2P4Sj0kksjvsBP8euIIppLBvrgdHiC7ptRZqiOh5blrLoL9QijDex7KhQ oFA2vLBV0d+bFGsq7hwlFQFmgteZg2y2/wqiSH1ao4O+MQ/tcRapjFJIDhETs8kB fKlHBuSKC0X1RMIL7kT74hme0MxflR8= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from venus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (venus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id mwJMvCQ7fEtU; Wed, 22 Nov 2017 12:34:45 +0100 (CET) Received: from HTCAONE.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1 with cipher ECDHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTPS; Wed, 22 Nov 2017 12:34:45 +0100 (CET) Received: from banana.mdc-berlin.net (141.80.180.135) by HTCAONE.mdc-berlin.net (141.80.180.125) with Microsoft SMTP Server (TLS) id 14.3.361.1; Wed, 22 Nov 2017 12:34:28 +0100 From: To: <29394@debbugs.gnu.org> Subject: [PATCH 10/12] gnu: Add ant-junit. Date: Wed, 22 Nov 2017 12:30:40 +0100 Message-ID: <20171122113042.1734-10-ricardo.wurmus@mdc-berlin.de> X-Mailer: git-send-email 2.15.0 In-Reply-To: <20171122113042.1734-1-ricardo.wurmus@mdc-berlin.de> References: <20171122113042.1734-1-ricardo.wurmus@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.180.135] X-TM-AS-Product-Ver: SMEX-11.0.0.4283-8.100.1062-23482.005 X-TM-AS-Result: No--1.791500-0.000000-31 X-TM-AS-MatchedID: 700486-703786-704425-188019-702015-700502-704421-188198-7 02106-105040-300015-709251-703720-862883-847575-106420-148004-148036-29997- 42000-42003-63 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 29394 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.0 (-----) From: Ricardo Wurmus * gnu/packages/java.scm (ant-junit): New variable. --- gnu/packages/java.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index eca23d9da..8cf723074 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -1784,6 +1784,38 @@ IcedTea build harness.") `(("java-commons-bcel" ,java-commons-bcel) ,@(package-inputs ant/java8))))) +(define-public ant-junit + (package + (inherit ant/java8) + (name "ant-junit") + (arguments + (substitute-keyword-arguments (package-arguments ant/java8) + ((#:phases phases) + `(modify-phases ,phases + (add-after 'unpack 'link-junit + (lambda* (#:key inputs #:allow-other-keys) + (for-each (lambda (file) + (symlink file + (string-append "lib/optional/" + (basename file)))) + (find-files (assoc-ref inputs "java-junit") + "\\.jar$")) + #t)) + (add-after 'build 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (share (string-append out "/share/java")) + (bin (string-append out "/bin")) + (lib (string-append out "/lib"))) + (mkdir-p share) + (install-file (string-append lib "/ant-junit.jar") share) + (delete-file-recursively bin) + (delete-file-recursively lib) + #t))))))) + (inputs + `(("java-junit" ,java-junit) + ,@(package-inputs ant/java8))))) + (define-public clojure (let* ((remove-archives '(begin (for-each delete-file -- 2.14.1 From debbugs-submit-bounces@debbugs.gnu.org Wed Nov 22 06:34:51 2017 Received: (at 29394) by debbugs.gnu.org; 22 Nov 2017 11:34:51 +0000 Received: from localhost ([127.0.0.1]:51941 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1eHTIp-0007zf-BH for submit@debbugs.gnu.org; Wed, 22 Nov 2017 06:34:51 -0500 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:36086) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1eHTIl-0007zO-Pm for 29394@debbugs.gnu.org; Wed, 22 Nov 2017 06:34:48 -0500 Received: from localhost (localhost [127.0.0.1]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 41FDD380B9F; Wed, 22 Nov 2017 12:34:47 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:references:in-reply-to :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1511350486; x=1513164887; bh=jWZMHEI2CkcIfGbLZwcdCt1YCHIxgI3s1A4gCoJc13U=; b=jZ4WgOZTPe8g RFsh901+bzt8elI1g9KOot+yfdJYWvCJYtIDaE9qPfbLCGiZ4SGsw1R1EepJJYI1 CoTn499GvrPR31d9U/uBwF/kIOc7+dhKD6K54+gK5oecvDcbjRU/o//w/iaxJGIR hGcdPX3YeQo0vkYRpxkwPGPsj+hexw0= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from venus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (venus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id hNbeV-supXuK; Wed, 22 Nov 2017 12:34:46 +0100 (CET) Received: from HTCAONE.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1 with cipher ECDHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTPS; Wed, 22 Nov 2017 12:34:46 +0100 (CET) Received: from banana.mdc-berlin.net (141.80.180.135) by HTCAONE.mdc-berlin.net (141.80.180.125) with Microsoft SMTP Server (TLS) id 14.3.361.1; Wed, 22 Nov 2017 12:34:46 +0100 From: To: <29394@debbugs.gnu.org> Subject: [PATCH 11/12] gnu: Add java-picard-1.113. Date: Wed, 22 Nov 2017 12:30:41 +0100 Message-ID: <20171122113042.1734-11-ricardo.wurmus@mdc-berlin.de> X-Mailer: git-send-email 2.15.0 In-Reply-To: <20171122113042.1734-1-ricardo.wurmus@mdc-berlin.de> References: <20171122113042.1734-1-ricardo.wurmus@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.180.135] X-TM-AS-Product-Ver: SMEX-11.0.0.4283-8.100.1062-23482.005 X-TM-AS-Result: No--3.774200-0.000000-31 X-TM-AS-MatchedID: 700486-703786-704425-188019-707997-704496-701590-706817-1 39705-709251-701762-847575-700970-700079-703283-106230-105250-702020-705098 -704852-701407-706561-702358-704421-188198-702106-105040-705178-700324-7045 78-709908-703176-700748-707909-700648-701719-188199-706803-702015-148004-14 8036-29997-42000-42003-63 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 29394 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.0 (-----) From: Ricardo Wurmus * gnu/packages/bioinformatics.scm (java-picard-1.113): New variable. --- gnu/packages/bioinformatics.scm | 114 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 114 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0896edf25..16e20c189 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3086,6 +3086,120 @@ commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and VCF.") (license license:expat))) +;; This is the last version of Picard to provide net.sf.samtools +(define-public java-picard-1.113 + (package (inherit java-picard) + (name "java-picard") + (version "1.113") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/broadinstitute/picard.git") + (commit version))) + (file-name (string-append "java-picard-" version "-checkout")) + (sha256 + (base32 + "0lkpvin2fz3hhly4l02kk56fqy8lmlgyzr9kmvljk6ry6l1hw973")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Delete pre-built binaries. + (delete-file-recursively "lib") + (mkdir-p "lib") + #t)))) + (build-system ant-build-system) + (arguments + `(#:build-target "picard-jar" + #:test-target "test" + ;; FIXME: the class path at test time is wrong. + ;; [testng] Error: A JNI error has occurred, please check your installation and try again + ;; [testng] Exception in thread "main" java.lang.NoClassDefFoundError: com/beust/jcommander/ParameterException + #:tests? #f + #:jdk ,icedtea-8 + ;; This is only used for tests. + #:make-flags + (list "-Dsamjdk.intel_deflater_so_path=lib/jni/libIntelDeflater.so") + #:phases + (modify-phases %standard-phases + ;; Do not use bundled ant bzip2. + (add-after 'unpack 'use-ant-bzip + (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)) + (add-after 'unpack 'make-test-target-independent + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "build.xml" + (("name=\"test\" depends=\"compile, ") + "name=\"test\" depends=\"compile-tests, ") + (("name=\"compile\" depends=\"compile-src, compile-tests\"") + "name=\"compile\" depends=\"compile-src\"")) + #t)) + (add-after 'unpack 'fix-deflater-path + (lambda* (#:key outputs #:allow-other-keys) + (substitute* "src/java/net/sf/samtools/Defaults.java" + (("getStringProperty\\(\"intel_deflater_so_path\", null\\)") + (string-append "getStringProperty(\"intel_deflater_so_path\", \"" + (assoc-ref outputs "out") + "/lib/jni/libIntelDeflater.so" + "\")"))) + #t)) + ;; Build the deflater library, because we've previously deleted the + ;; pre-built one. This can only be built with access to the JDK + ;; sources. + (add-after 'build 'build-jni + (lambda* (#:key inputs #:allow-other-keys) + (mkdir-p "lib/jni") + (mkdir-p "jdk-src") + (and (zero? (system* "tar" "--strip-components=1" "-C" "jdk-src" + "-xf" (assoc-ref inputs "jdk-src"))) + (zero? (system* "javah" "-jni" + "-classpath" "classes" + "-d" "lib/" + "net.sf.samtools.util.zip.IntelDeflater")) + (with-directory-excursion "src/c/inteldeflater" + (zero? (system* "gcc" "-I../../../lib" "-I." + (string-append "-I" (assoc-ref inputs "jdk") + "/include/linux") + "-I../../../jdk-src/src/share/native/common/" + "-I../../../jdk-src/src/solaris/native/common/" + "-c" "-O3" "-fPIC" "IntelDeflater.c")) + (zero? (system* "gcc" "-shared" + "-o" "../../../lib/jni/libIntelDeflater.so" + "IntelDeflater.o" "-lz" "-lstdc++")))))) + ;; We can only build everything else after building the JNI library. + (add-after 'build-jni 'build-rest + (lambda* (#:key make-flags #:allow-other-keys) + (zero? (apply system* `("ant" "all" ,@make-flags))))) + (add-before 'build 'set-JAVA6_HOME + (lambda _ + (setenv "JAVA6_HOME" (getenv "JAVA_HOME")) + #t)) + (replace 'install (install-jars "dist")) + (add-after 'install 'install-jni-lib + (lambda* (#:key outputs #:allow-other-keys) + (let ((jni (string-append (assoc-ref outputs "out") + "/lib/jni"))) + (mkdir-p jni) + (install-file "lib/jni/libIntelDeflater.so" jni) + #t)))))) + (inputs + `(("java-snappy-1" ,java-snappy-1) + ("java-commons-jexl-2" ,java-commons-jexl-2) + ("java-cofoja" ,java-cofoja) + ("ant" ,ant) ; for bzip2 support at runtime + ("zlib" ,zlib))) + (native-inputs + `(("ant-apache-bcel" ,ant-apache-bcel) + ("ant-junit" ,ant-junit) + ("java-testng" ,java-testng) + ("java-commons-bcel" ,java-commons-bcel) + ("java-jcommander" ,java-jcommander) + ("jdk" ,icedtea-8 "jdk") + ("jdk-src" ,(car (assoc-ref (package-native-inputs icedtea-8) "jdk-drop"))))))) + (define-public htslib (package (name "htslib") -- 2.14.1 From debbugs-submit-bounces@debbugs.gnu.org Wed Nov 22 06:34:56 2017 Received: (at 29394) by debbugs.gnu.org; 22 Nov 2017 11:34:56 +0000 Received: from localhost ([127.0.0.1]:51944 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1eHTIt-0007zw-Ox for submit@debbugs.gnu.org; Wed, 22 Nov 2017 06:34:55 -0500 Received: from pegasus.bbbm.mdc-berlin.de ([141.80.25.20]:33034) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1eHTIs-0007zo-9q for 29394@debbugs.gnu.org; Wed, 22 Nov 2017 06:34:54 -0500 Received: from localhost (localhost [127.0.0.1]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 6F400511D80; Wed, 22 Nov 2017 12:34:53 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:references:in-reply-to :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1511350488; x=1513164889; bh=LoZdNak2Tgxy7NY9JNNm6JI8nmMONr/3DbCD5iW0c6I=; b=T+N7QIgBHRib Z/eAfAAqdIngIoEaWEAZyM4g3bQ2Qlwse6XuK5iyIsmkAJ1f5rW91kzgAbZmK9uv krxOB20tX6jjTVCKb2W6egyMJ4Ppls4HWwbCvW/y+PJeSF32mHaknYIQWIGzBZTS jvP8KwaLlCefym2Kgx7dB+1y50TSGbA= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from pegasus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (pegasus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 0Q0kw5-PlwwD; Wed, 22 Nov 2017 12:34:48 +0100 (CET) Received: from HTCAONE.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1 with cipher ECDHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTPS; Wed, 22 Nov 2017 12:34:48 +0100 (CET) Received: from banana.mdc-berlin.net (141.80.180.135) by HTCAONE.mdc-berlin.net (141.80.180.125) with Microsoft SMTP Server (TLS) id 14.3.361.1; Wed, 22 Nov 2017 12:34:47 +0100 From: To: <29394@debbugs.gnu.org> Subject: [PATCH 12/12] gnu: Add java-jbzip2. Date: Wed, 22 Nov 2017 12:30:42 +0100 Message-ID: <20171122113042.1734-12-ricardo.wurmus@mdc-berlin.de> X-Mailer: git-send-email 2.15.0 In-Reply-To: <20171122113042.1734-1-ricardo.wurmus@mdc-berlin.de> References: <20171122113042.1734-1-ricardo.wurmus@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.180.135] X-TM-AS-Product-Ver: SMEX-11.0.0.4283-8.100.1062-23482.005 X-TM-AS-Result: No--10.915500-0.000000-31 X-TM-AS-MatchedID: 700486-703786-704425-188019-701604-188199-702474-704496-7 01590-706817-709251-139705-702150-701407-700630-706561-704421-705178-863828 -139504-702010-702609-711380-188198-704568-700840-700748-148004-148036-4200 0-42003-63 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 29394 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.0 (-----) From: Ricardo Wurmus * gnu/packages/compression.scm (java-jbzip2): New variable. --- gnu/packages/compression.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index 193d36797..4ea4b105f 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -1314,6 +1314,46 @@ Java. This compression code produces a byte-for-byte exact copy of the output created by the original C++ code, and extremely fast.") (license license:asl2.0))) +(define-public java-jbzip2 + (package + (name "java-jbzip2") + (version "0.9.1") + (source (origin + (method url-fetch) + (uri (string-append "https://storage.googleapis.com/" + "google-code-archive-source/v2/" + "code.google.com/jbzip2/" + "source-archive.zip")) + (file-name (string-append name "-" version ".zip")) + (sha256 + (base32 + "0ncmhlqmrfmj96nqf6p77b9ws35lcfsvpfxzwxi2asissc83z1l3")))) + (build-system ant-build-system) + (native-inputs + `(("unzip" ,unzip) + ("java-junit" ,java-junit))) + (arguments + `(#:tests? #f ; no tests + #:jar-name "jbzip2.jar" + #:source-dir "tags/release-0.9.1/src" + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-encoding-problems + (lambda _ + ;; Some of the files we're patching are + ;; ISO-8859-1-encoded, so choose it as the default + ;; encoding so the byte encoding is preserved. + (with-fluids ((%default-port-encoding #f)) + (substitute* "tags/release-0.9.1/src/org/itadaki/bzip2/HuffmanAllocator.java" + (("Milidi.") "Milidiu"))) + #t))))) + (home-page "https://code.google.com/archive/p/jbzip2/") + (synopsis "Java bzip2 compression/decompression library") + (description "Jbzip2 is a Java bzip2 compression/decompression library. +It can be used as a replacement for the Apache @code{CBZip2InputStream} / +@code{CBZip2OutputStream} classes.") + (license license:expat))) + (define-public p7zip (package (name "p7zip") -- 2.14.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Nov 27 15:56:31 2017 Received: (at 29394-done) by debbugs.gnu.org; 27 Nov 2017 20:56:31 +0000 Received: from localhost ([127.0.0.1]:33139 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1eJQS7-0000cB-H6 for submit@debbugs.gnu.org; Mon, 27 Nov 2017 15:56:31 -0500 Received: from sinope02.bbbm.mdc-berlin.de ([141.80.25.24]:36340) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1eJQS5-0000c1-KB for 29394-done@debbugs.gnu.org; Mon, 27 Nov 2017 15:56:30 -0500 Received: from localhost (localhost [127.0.0.1]) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTP id 73499DD315F for <29394-done@debbugs.gnu.org>; Mon, 27 Nov 2017 21:56:28 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:message-id:date:date :in-reply-to:subject:subject:from:from:user-agent:references :received:received:received; s=mdc; t=1511816183; x=1513630584; bh=nS8GqbD1k5bV3yuwpgIsEZlxCkbniKp5CSqv0jBuSBY=; b=sT94p4XU1Qg1 bPLhBYGMTQ0B4bCBsSsheu1gg0ZcC856nXLF4QdFTFV5qefUCoVPgVBHB0plZb9e V2OfYq+zpuB74PaXX82e02mU1AUoAquNLiVgz1LGdomIpdj96RP3sFsRsqVRvtEL wL3PdITFS5zbS6Et1DbOzf4mzmtxWCs= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from sinope02.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope02.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id grjhih24Z4Fc for <29394-done@debbugs.gnu.org>; Mon, 27 Nov 2017 21:56:23 +0100 (CET) Received: from HTCAONE.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1 with cipher ECDHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTPS for <29394-done@debbugs.gnu.org>; Mon, 27 Nov 2017 21:56:22 +0100 (CET) Received: from localhost (141.80.180.135) by HTCAONE.mdc-berlin.net (141.80.180.125) with Microsoft SMTP Server (TLS) id 14.3.361.1; Mon, 27 Nov 2017 21:56:21 +0100 References: <20171122113042.1734-1-ricardo.wurmus@mdc-berlin.de> <20171122113042.1734-12-ricardo.wurmus@mdc-berlin.de> User-agent: mu4e 0.9.18; emacs 25.3.1 From: Ricardo Wurmus To: <29394-done@debbugs.gnu.org> Subject: Re: [PATCH 12/12] gnu: Add java-jbzip2. In-Reply-To: <20171122113042.1734-12-ricardo.wurmus@mdc-berlin.de> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Mon, 27 Nov 2017 21:56:21 +0100 Message-ID: <87609vqw3u.fsf@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.180.135] X-TM-AS-Product-Ver: SMEX-11.0.0.4283-8.100.1062-23496.002 X-TM-AS-Result: No--0.351300-0.000000-31 X-TM-AS-MatchedID: 150567-703330-148004-148036-10005-10016-10114-41002-42000-42003-63 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 29394-done X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.0 (/) Pushed them all to the master branch. -- Ricardo From unknown Fri Sep 05 15:36:55 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Tue, 26 Dec 2017 12:24:06 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator