Attachment #238321 for bug #247337

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PORTNAME=	cytoscape
DISTVERSION=	3.9.1
CATEGORIES=	biology java
MASTER_SITES=	LOCAL/yuri/:maven \
		http://people.freebsd.org/~yuri/:maven
DISTFILES=	FreeBSD-${PORTNAME}-${PORTVERSION}-maven-repository.tar.gz:maven

MAINTAINER=	yuri@FreeBSD.org
COMMENT=	Software to visualize molecular interaction networks, gene expression

LICENSE=	LGPL21
LICENSE_FILE=	${WRKSRC}/api/LICENSE

BROKEN=		fails to build: Cytoscape Third-Party Dependencies (third-party): FAILURE

BUILD_DEPENDS=	mvn:devel/maven \
		bash:shells/bash
RUN_DEPENDS=	bash:shells/bash

SHEBANG_FILES=	gui-distribution/assembly/src/main/bin/cytoscape.sh
USE_JAVA=	yes
USE_GITHUB=	yes
GH_TUPLE=	${PORTNAME}:${PORTNAME}-parent:3.8.2:p/parent \
		${PORTNAME}:${PORTNAME}-api:3.8.2:a/api \
		${PORTNAME}:${PORTNAME}-impl:3.8.2:i/impl \
		${PORTNAME}:${PORTNAME}-support:3.8.2:s/support \
		${PORTNAME}:${PORTNAME}-gui-distribution:3.8.2:g/gui-distribution \
		${PORTNAME}:${PORTNAME}-app-template:3.9.0:d/app-developer
NO_ARCH=	yes

USER_WRKDIR=	~/.${PORTNAME}

# to rebuild the deps archive:
#   1. set DEV_UPDATE_MODE=yes
#   2. make makesum build
#   3. upload the *-deps archive
#   4. set DEV_UPDATE_MODE=no
#   5. make clean makesum

DEV_UPDATE_MODE=	yes

.if (${DEV_UPDATE_MODE} == "yes")
post-build:
	@cd ${WRKDIR} && ${TAR} czf ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX} .m2
	@${ECHO} "(!!!) Please upload the maven deps archive: ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}"
.else
MASTER_SITES+=	LOCAL/yuri/:maven
DISTFILES+=	${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}:maven
MVN_ARGS=	--offline
.endif

do-build:
	@cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} \
		${LOCALBASE}/bin/mvn ${MVN_ARGS} \
		-fae install \
		-Dmaven.test.skip=true \
		-Duser.home=${WRKDIR}




TIMESTAMP = 1669316799
SHA256 (cytoscape-cytoscape-3.9.1_GH0.tar.gz) = 968f0966b87daff4e1d71e5864564b16c4fc437eeb61870cb8b69a6db33c657e
SIZE (cytoscape-cytoscape-3.9.1_GH0.tar.gz) = 15936
SHA256 (cytoscape-cytoscape-parent-3.8.2_GH0.tar.gz) = 8adb145657923851f90e30289ac2f5a38a73899893ed67013d7f47a8a5921361
SIZE (cytoscape-cytoscape-parent-3.8.2_GH0.tar.gz) = 3888
SHA256 (cytoscape-cytoscape-api-3.8.2_GH0.tar.gz) = 7ae943933e58c4e389144ff2ce8c378d6cb6ae2d6044d11d38e86540b6f57100
SIZE (cytoscape-cytoscape-api-3.8.2_GH0.tar.gz) = 1766800
SHA256 (cytoscape-cytoscape-impl-3.8.2_GH0.tar.gz) = 247841fc40be5cc7b4a1242df7ac00728b3d1cd718bdc50f6904a30bd95170c4
SIZE (cytoscape-cytoscape-impl-3.8.2_GH0.tar.gz) = 34000656
SHA256 (cytoscape-cytoscape-support-3.8.2_GH0.tar.gz) = d34e89d62a8e7635d330b0695a0137c24f1cd902601714df1596dae77132d537
SIZE (cytoscape-cytoscape-support-3.8.2_GH0.tar.gz) = 53831
SHA256 (cytoscape-cytoscape-gui-distribution-3.8.2_GH0.tar.gz) = 11a38848929651d717429028b4e10339f5d529701ce89b4de8112ca71e48d05d
SIZE (cytoscape-cytoscape-gui-distribution-3.8.2_GH0.tar.gz) = 14480707
SHA256 (cytoscape-cytoscape-app-template-3.9.0_GH0.tar.gz) = 8d99724a8c03cee75a6c99f52513ac2346d32f67e3fb3a4c59acdc99cd5261e3
SIZE (cytoscape-cytoscape-app-template-3.9.0_GH0.tar.gz) = 1880
SHA256 (cytoscape-cytoscape-gui-distribution-3.6.1_GH0.tar.gz) = 73fb7efb51a0413252a7e9e28d4fb7e28d16eea9f60be534fd962a5e534ca72e
SIZE (cytoscape-cytoscape-gui-distribution-3.6.1_GH0.tar.gz) = 14818052
SHA256 (cytoscape-cytoscape-app-template-3.6.1_GH0.tar.gz) = 9cf7b64a3e6effd22a20d577c7fa41b11f896e2298ef1655f2fe31c21602bce0
SIZE (cytoscape-cytoscape-app-template-3.6.1_GH0.tar.gz) = 1887

Return to bug 247337

Lines 1-9 Link Here

(-)b/biology/cytoscape/Makefile (-13 / +27 lines)
1	PORTNAME= cytoscape	1	PORTNAME= cytoscape
2	DISTVERSION= 3.6.1	2	DISTVERSION= 3.9.1
3	CATEGORIES= biology java	3	CATEGORIES= biology java
4	MASTER_SITES= LOCAL/yuri/:maven \
5	http://people.freebsd.org/~yuri/:maven
6	DISTFILES= FreeBSD-${PORTNAME}-${PORTVERSION}-maven-repository.tar.gz:maven
7		4
8	MAINTAINER= yuri@FreeBSD.org	5	MAINTAINER= yuri@FreeBSD.org
9	COMMENT= Software to visualize molecular interaction networks, gene expression	6	COMMENT= Software to visualize molecular interaction networks, gene expression
Lines 12-19 WWW= https://www.cytoscape.org Link Here
12	LICENSE= LGPL21	9	LICENSE= LGPL21
13	LICENSE_FILE= ${WRKSRC}/api/LICENSE	10	LICENSE_FILE= ${WRKSRC}/api/LICENSE
14		11
15	BROKEN= fails to build: Cytoscape Third-Party Dependencies (third-party): FAILURE
16
17	BUILD_DEPENDS= mvn:devel/maven \	12	BUILD_DEPENDS= mvn:devel/maven \
18	bash:shells/bash	13	bash:shells/bash
19	RUN_DEPENDS= bash:shells/bash	14	RUN_DEPENDS= bash:shells/bash
Lines 22-40 USES= shebangfix Link Here
22	SHEBANG_FILES= gui-distribution/assembly/src/main/bin/cytoscape.sh	17	SHEBANG_FILES= gui-distribution/assembly/src/main/bin/cytoscape.sh
23	USE_JAVA= yes	18	USE_JAVA= yes
24	USE_GITHUB= yes	19	USE_GITHUB= yes
25	GH_TUPLE= ${PORTNAME}:${PORTNAME}-parent:${DISTVERSION}:p/parent \	20	GH_TUPLE= ${PORTNAME}:${PORTNAME}-parent:3.8.2:p/parent \
26	${PORTNAME}:${PORTNAME}-api:${DISTVERSION}:a/api \	21	${PORTNAME}:${PORTNAME}-api:3.8.2:a/api \
27	${PORTNAME}:${PORTNAME}-impl:${DISTVERSION}:i/impl \	22	${PORTNAME}:${PORTNAME}-impl:3.8.2:i/impl \
28	${PORTNAME}:${PORTNAME}-support:${DISTVERSION}:s/support \	23	${PORTNAME}:${PORTNAME}-support:3.8.2:s/support \
29	${PORTNAME}:${PORTNAME}-gui-distribution:${DISTVERSION}:g/gui-distribution \	24	${PORTNAME}:${PORTNAME}-gui-distribution:3.8.2:g/gui-distribution \
30	${PORTNAME}:${PORTNAME}-app-template:${DISTVERSION}:d/app-developer	25	${PORTNAME}:${PORTNAME}-app-template:3.9.0:d/app-developer
31	NO_ARCH= yes	26	NO_ARCH= yes
32		27
33	USER_WRKDIR= ~/.${PORTNAME}	28	USER_WRKDIR= ~/.${PORTNAME}
34		29
		30	# to rebuild the deps archive:
		31	# 1. set DEV_UPDATE_MODE=yes
		32	# 2. make makesum build
		33	# 3. upload the *-deps archive
		34	# 4. set DEV_UPDATE_MODE=no
		35	# 5. make clean makesum
		36
		37	DEV_UPDATE_MODE= yes
		38
		39	.if (${DEV_UPDATE_MODE} == "yes")
		40	post-build:
		41	@cd ${WRKDIR} && ${TAR} czf ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX} .m2
		42	@${ECHO} "(!!!) Please upload the maven deps archive: ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}"
		43	.else
		44	MASTER_SITES+= LOCAL/yuri/:maven
		45	DISTFILES+= ${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}:maven
		46	MVN_ARGS= --offline
		47	.endif
		48
35	do-build:	49	do-build:
36	@cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} \	50	@cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} \
37	${LOCALBASE}/bin/mvn --offline \	51	${LOCALBASE}/bin/mvn ${MVN_ARGS} \
38	-fae install \	52	-fae install \
39	-Dmaven.test.skip=true \	53	-Dmaven.test.skip=true \
40	-Duser.home=${WRKDIR}	54	-Duser.home=${WRKDIR}

Lines 1-19 Link Here

(-)b/biology/cytoscape/distinfo (-19 / +15 lines)
1	TIMESTAMP = 1530956058	1	TIMESTAMP = 1669316799
2	SHA256 (FreeBSD-cytoscape-3.6.1-maven-repository.tar.gz) = f3e33e99168b56768d2ee854956e59bcbb888101fd518239887524d692b78f7a	2	SHA256 (cytoscape-cytoscape-3.9.1_GH0.tar.gz) = 968f0966b87daff4e1d71e5864564b16c4fc437eeb61870cb8b69a6db33c657e
3	SIZE (FreeBSD-cytoscape-3.6.1-maven-repository.tar.gz) = 1235655281	3	SIZE (cytoscape-cytoscape-3.9.1_GH0.tar.gz) = 15936
4	SHA256 (install4j-maven-plugin-1.1.1.jar) = 301f5ca0718e630a62583561fb1a05c26ee40b5dc81ddd1ffc56bb17c813c506	4	SHA256 (cytoscape-cytoscape-parent-3.8.2_GH0.tar.gz) = 8adb145657923851f90e30289ac2f5a38a73899893ed67013d7f47a8a5921361
5	SIZE (install4j-maven-plugin-1.1.1.jar) = 27105	5	SIZE (cytoscape-cytoscape-parent-3.8.2_GH0.tar.gz) = 3888
6	SHA256 (cytoscape-cytoscape-3.6.1_GH0.tar.gz) = f172c9e459293661a83d2618da511901410336b76b0c1716697e60f821c2f150	6	SHA256 (cytoscape-cytoscape-api-3.8.2_GH0.tar.gz) = 7ae943933e58c4e389144ff2ce8c378d6cb6ae2d6044d11d38e86540b6f57100
7	SIZE (cytoscape-cytoscape-3.6.1_GH0.tar.gz) = 12785	7	SIZE (cytoscape-cytoscape-api-3.8.2_GH0.tar.gz) = 1766800
8	SHA256 (cytoscape-cytoscape-parent-3.6.1_GH0.tar.gz) = 0786e8d7877fa54d2a64d65209856a4a946df4facd3cbc947e8c65d14a035084	8	SHA256 (cytoscape-cytoscape-impl-3.8.2_GH0.tar.gz) = 247841fc40be5cc7b4a1242df7ac00728b3d1cd718bdc50f6904a30bd95170c4
9	SIZE (cytoscape-cytoscape-parent-3.6.1_GH0.tar.gz) = 2863	9	SIZE (cytoscape-cytoscape-impl-3.8.2_GH0.tar.gz) = 34000656
10	SHA256 (cytoscape-cytoscape-api-3.6.1_GH0.tar.gz) = a264a434d5942cad2ef69df7aa29fad74a6d1f11369a964d7c38462608def73b	10	SHA256 (cytoscape-cytoscape-support-3.8.2_GH0.tar.gz) = d34e89d62a8e7635d330b0695a0137c24f1cd902601714df1596dae77132d537
11	SIZE (cytoscape-cytoscape-api-3.6.1_GH0.tar.gz) = 1731631	11	SIZE (cytoscape-cytoscape-support-3.8.2_GH0.tar.gz) = 53831
12	SHA256 (cytoscape-cytoscape-impl-3.6.1_GH0.tar.gz) = 0fcea5a4d804972db5b0cf77174a953d22da8fed6740dbaa01754eb7aea50d21	12	SHA256 (cytoscape-cytoscape-gui-distribution-3.8.2_GH0.tar.gz) = 11a38848929651d717429028b4e10339f5d529701ce89b4de8112ca71e48d05d
13	SIZE (cytoscape-cytoscape-impl-3.6.1_GH0.tar.gz) = 29851040	13	SIZE (cytoscape-cytoscape-gui-distribution-3.8.2_GH0.tar.gz) = 14480707
14	SHA256 (cytoscape-cytoscape-support-3.6.1_GH0.tar.gz) = 3f13088c35d41fa616dc7e735469f360ee4d17b1838cde8291f88b01bacfe657	14	SHA256 (cytoscape-cytoscape-app-template-3.9.0_GH0.tar.gz) = 8d99724a8c03cee75a6c99f52513ac2346d32f67e3fb3a4c59acdc99cd5261e3
15	SIZE (cytoscape-cytoscape-support-3.6.1_GH0.tar.gz) = 52940	15	SIZE (cytoscape-cytoscape-app-template-3.9.0_GH0.tar.gz) = 1880
16	SHA256 (cytoscape-cytoscape-gui-distribution-3.6.1_GH0.tar.gz) = 73fb7efb51a0413252a7e9e28d4fb7e28d16eea9f60be534fd962a5e534ca72e
17	SIZE (cytoscape-cytoscape-gui-distribution-3.6.1_GH0.tar.gz) = 14818052
18	SHA256 (cytoscape-cytoscape-app-template-3.6.1_GH0.tar.gz) = 9cf7b64a3e6effd22a20d577c7fa41b11f896e2298ef1655f2fe31c21602bce0
19	SIZE (cytoscape-cytoscape-app-template-3.6.1_GH0.tar.gz) = 1887