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Differential D13574

[new port] biology/canu: Single molecule sequence assembler
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Authored by jwb on Dec 21 2017, 4:53 PM.
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mat

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jrm
wen
koobs
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rP456982: biology/canu: Replace += with = for depends
rP456950: [new port] biology/canu: Single molecule sequence assembler
Summary

[new port] biology/canu: Single molecule sequence assembler
Approved by: jrm (mentor) or wen (mentor)
Differential to be added to log

Upstream has already patched head to conform to filesystem hierarchy standards, so the post-build hacks will go away in 1.7.

Test Plan

portlint -C and stage-qa clean
Poudriere tested on {10.3,11.1}-{amd64,i386}

User-tested by researchers

Diff Detail

Repository
rP FreeBSD ports repository
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No Lint Coverage
Unit
No Test Coverage
Build Status
Buildable 13744
Build 13964: arc lint + arc unit

Event Timeline

jwb created this revision.Dec 21 2017, 4:53 PM
Herald added a subscriber: mat. · View Herald TranscriptDec 21 2017, 4:53 PM
jwb edited the test plan for this revision. (Show Details)Dec 22 2017, 12:09 AM
jrm accepted this revision.Dec 22 2017, 12:13 AM
jrm added inline comments.
biology/canu/Makefile
4

missing tab?

This revision is now accepted and ready to land.Dec 22 2017, 12:13 AM
jwb updated this revision to Diff 36897.Dec 22 2017, 1:27 AM

Added that to my checklist

This revision now requires review to proceed.Dec 22 2017, 1:27 AM
jrm accepted this revision.Dec 22 2017, 1:29 AM
This revision is now accepted and ready to land.Dec 22 2017, 1:29 AM
Closed by commit rP456950: [new port] biology/canu: Single molecule sequence assembler (authored by jwb). · Explain WhyDec 22 2017, 1:30 AM
This revision was automatically updated to reflect the committed changes.
mat added inline comments.Dec 22 2017, 8:36 AM
head/biology/canu/Makefile
14–15 ↗(On Diff #36898)

Why += ?

head/biology/canu/pkg-plist
54–55 ↗(On Diff #36898)

installing only static libraries seems like a bad idea.

jwb reopened this revision.Dec 22 2017, 1:42 PM
jwb updated this revision to Diff 36906.Dec 22 2017, 1:45 PM

Good catch on the +=, that was an oversight.

The upstream build system does not support shared libs and it's a nightmare
to patch. The developers are receptive to suggestion, though. I plan to
open an issue asking for shared libs in a future release.

Harbormaster completed remote builds in B13744: Diff 36906.Dec 22 2017, 1:45 PM
jrm accepted this revision.Dec 22 2017, 1:47 PM
This revision is now accepted and ready to land.Dec 22 2017, 1:47 PM
Closed by commit rP456982: biology/canu: Replace += with = for depends (authored by jwb). · Explain WhyDec 22 2017, 2:14 PM
This revision was automatically updated to reflect the committed changes.

Revision Contents
Changeset List

PathSize
biology/
canu/
4 lines

Diff 36906

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biology/canu/Makefile

# Created by: Alberto Villa <avilla@FreeBSD.org> # Created by: Alberto Villa <avilla@FreeBSD.org>
# $FreeBSD$ # $FreeBSD$
PORTNAME= telepathy-qt PORTNAME= telepathy-qt
PORTVERSION= 0.9.7 PORTVERSION= 0.9.7
PORTREVISION= 1
CATEGORIES= net-im CATEGORIES= net-im
MASTER_SITES= https://telepathy.freedesktop.org/releases/${PORTNAME}/ MASTER_SITES= https://telepathy.freedesktop.org/releases/${PORTNAME}/
PKGNAMESUFFIX?= 4 PKGNAMESUFFIX?= 4
MAINTAINER= kde@FreeBSD.org MAINTAINER= kde@FreeBSD.org
COMMENT= High-level Qt binding for Telepathy COMMENT= High-level Qt binding for Telepathy
LICENSE= LGPL21 LICENSE= LGPL21
Show All 9 Lines
USE_GSTREAMER= yes USE_GSTREAMER= yes
USES= cmake:outsource gettext pathfix pkgconfig python:build USES= cmake:outsource gettext pathfix pkgconfig python:build
CMAKE_ARGS= -DENABLE_EXAMPLES:BOOL=False \ CMAKE_ARGS= -DENABLE_EXAMPLES:BOOL=False \
-DENABLE_FARSIGHT:BOOL=False \ -DENABLE_FARSIGHT:BOOL=False \
-DENABLE_FARSTREAM:BOOL=True \ -DENABLE_FARSTREAM:BOOL=True \
-DENABLE_TESTS:BOOL=False \ -DENABLE_TESTS:BOOL=False \
-DDESIRED_QT_VERSION:STRING=${PKGNAMESUFFIX} \ -DDESIRED_QT_VERSION:STRING=${PKGNAMESUFFIX} \
-DQT_QMAKE_EXECUTABLE:FILEPATH=${QMAKE} -DQT_QMAKE_EXECUTABLE:FILEPATH=${QMAKE}
. if ${PKGNAMESUFFIX:M4} . if ${PKGNAMESUFFIX:M4}
jbeichUnsubmitted
Not Done
Inline Actions

This could have been expressed in a more declarative style e.g.,

# master
OPTIONS_SLAVE?=	QT4

QT4_USE=	QT4=corelib,dbus,...
QT4_PLIST_SUB=	SHLIB_SUFFIX=2

QT5_USE=	QT5=core,dbus,...
QT5_PLIST_SUB=	SHLIB_SUFFIX=0

# slave
OPTIONS_SLAVE=	QT5
jbeich: This could have been expressed in a more declarative style e.g., ```lang=bsdmake # master…
USE_QT4= corelib dbus gui network qtestlib_build xml \ USE_QT4= corelib dbus gui network qtestlib_build xml \
moc_build qmake_build rcc_build uic_build moc_build qmake_build rcc_build uic_build
SHLIB_SUFFIX= 2 SHLIB_SUFFIX= 2
. else . else
USE_QT5= core dbus gui network xml \ USE_QT5= core dbus gui network xml \
buildtools_build qmake_build testlib_build widgets_build buildtools_build qmake_build testlib_build widgets_build
SHLIB_SUFFIX= 0 SHLIB_SUFFIX= 0
. endif . endif
Show All 10 Lines
CMAKE_ARGS+= -DDOXYGEN_EXECUTABLE:FILEPATH="" CMAKE_ARGS+= -DDOXYGEN_EXECUTABLE:FILEPATH=""
PLIST_SUB= PORTVERSION="${PORTVERSION}" \ PLIST_SUB= PORTVERSION="${PORTVERSION}" \
QTVER_SUFFIX="${PKGNAMESUFFIX}" \ QTVER_SUFFIX="${PKGNAMESUFFIX}" \
SHLIB_SUFFIX="${SHLIB_SUFFIX}" SHLIB_SUFFIX="${SHLIB_SUFFIX}"
PORTDOCS= AUTHORS ChangeLog HACKING NEWS README html PORTDOCS= AUTHORS ChangeLog HACKING NEWS README html
# Manually set DOCSDIR, to handle the version suffix # Manually set DOCSDIR, to handle the version suffix
DOCSDIR= ${PREFIX}/usr/share/${PORTNAME}${PKGNAMESUFFIX} DOCSDIR= ${PREFIX}/share/doc/${PORTNAME}${PKGNAMESUFFIX}
jbeichUnsubmitted
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Inline Actions

Breaking statu quo requires PORTREVISION bump: /doc suffix is gone while /usr added.

$ svn up -r423331
$ make -V DOCSDIR
/usr/local/share/doc/telepathy-qt4

$ svn up -r423332
$ make -V DOCSDIR
/usr/local/usr/share/telepathy-qt4
jbeich: Breaking statu quo requires `PORTREVISION` bump: `/doc` suffix is gone while `/usr` added.
tcbernerAuthorUnsubmitted
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Inline Actions

Yikes. You're completely right. That is wrong.

I'll provide a correct update as soon as I can.

tcberner: Yikes. You're completely right. That is wrong. I'll provide a correct update as soon as I can.
post-install-DOCS-on: post-install-DOCS-on:
${MKDIR} ${STAGEDIR}${DOCSDIR} ${MKDIR} ${STAGEDIR}${DOCSDIR}
cd ${WRKSRC} && ${CP} -R doc/html . cd ${WRKSRC} && ${CP} -R doc/html .
. for f in ${PORTDOCS} . for f in ${PORTDOCS}
cd ${WRKSRC} && ${COPYTREE_SHARE} ${f} ${STAGEDIR}${DOCSDIR} cd ${WRKSRC} && ${COPYTREE_SHARE} ${f} ${STAGEDIR}${DOCSDIR}
. endfor . endfor
.include <bsd.port.mk> .include <bsd.port.mk>