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biology/tabixpp: C++ wrapper to tabix indexer
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Authored by jwb on Apr 5 2018, 4:13 PM.
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jrm
wen
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rP467343: biology/tabixpp: C++ wrapper to tabix indexer
Summary

biology/tabixpp: C++ wrapper to tabix indexer

First of several submodules for wip/vcflib that I unbundled. files/Makefile
is a generalized version of their Makefile that was not accepted by upstream.
They pulled a few of my merge requests for other things and then seemed to
lose interest in the idea of supporting package managers, so I think the
Makefile will have to live in the port.

Approved by jrm (mentor) or wen (mentor)
Differential to be added to commit message

Test Plan

portlint -A: looks fine
Passed poudriere on {10.3,11.1}-{amd64,i386}
Tested in production as dependency of ddocent

Diff Detail

Repository
rP FreeBSD ports repository
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No Lint Coverage
Unit
No Test Coverage
Build Status
Buildable 15997
Build 15979: arc lint + arc unit

Event Timeline

jwb created this revision.Apr 5 2018, 4:13 PM
Herald added a subscriber: mat. · View Herald TranscriptApr 5 2018, 4:13 PM
Harbormaster completed remote builds in B15994: Diff 41137.Apr 5 2018, 4:13 PM
jrm added inline comments.Apr 5 2018, 4:53 PM
biology/tabixpp/Makefile
5–6
DISTVERSIONPREFIX=	v
DISTVERSION=	1.0.0-10
7

-wip

17–20

I think the USES and USE_x block could be

USES=		localbase:ldflags
USE_GITHUB=	yes
GH_ACCOUNT=	ekg
USE_LDCONFIG=	yes

then the Standard bsd.port.mk Variables block could be

# Disable bundled htslib
MAKE_ENV=	HTS_HEADERS='' HTS_LIB=''
INSTALL_TARGET=	install-strip
PLIST_FILES=	bin/tabix++ \
		include/tabix.hpp \
		lib/libtabix.a \
		lib/libtabix.so \
		lib/libtabix.so.1
jwb updated this revision to Diff 41145.Apr 5 2018, 7:32 PM

localbase:ldflags is what I was looking for...

I was surprised I needed to ammend CXXFLAGS and LDFLAGS here. Have to explore
that a little further. Forgot to run port-check outside wip again, hence the
wip category. More distractions today. Thanks.

Harbormaster completed remote builds in B15997: Diff 41145.Apr 5 2018, 7:32 PM
mat added inline comments.Apr 5 2018, 10:08 PM
biology/tabixpp/Makefile
31–32
MAKEFILE=${FILESDIR}/Makefile
35

Possibly:

${RLN} ${STAGEDIR}${PREFIX}/libtabix.so.1 ${STAGEDIR}${PREFIX}/libtabix.so
jwb updated this revision to Diff 41177.Apr 6 2018, 1:48 PM

Interesting. I would not have thought to use anything outside WRKSRC in the
build.

With RLN:

install -l rs /usr/ports/biology/tabixpp/work/stage/usr/local/libtabix.so.1 /usr/ports/biology/tabixpp/work/stage/usr/local/libtabix.so
install: /usr/ports/biology/tabixpp/work/stage/usr/local/libtabix.so.1: realpath: No such file or directory

  • Error code 71

The RLN command is actually longer anyway, and wraps. I'm a neat freak so
I prefer the (cd ...) in this case.

Harbormaster completed remote builds in B16013: Diff 41177.Apr 6 2018, 1:48 PM
jrm added inline comments.Apr 6 2018, 2:42 PM
biology/tabixpp/Makefile
35

This works, it's just the path is wrong. It should be

${RLN} ${STAGEDIR}${PREFIX}/lib/libtabix.so.1 ${STAGEDIR}${PREFIX}/lib/libtabix.so

Apparently @mat is human.

See the "Handling Symbolic Links" section of the PH.

jrm accepted this revision.Apr 6 2018, 2:46 PM
This revision is now accepted and ready to land.Apr 6 2018, 2:46 PM
jwb updated this revision to Diff 41244.Apr 7 2018, 10:26 PM

Human because he expected me to notice the missing lib/? ;-)

On second thought, consistent use of available features trumps cosmetic
neatness.

This revision now requires review to proceed.Apr 7 2018, 10:26 PM
Harbormaster completed remote builds in B16046: Diff 41244.Apr 7 2018, 10:26 PM
jrm accepted this revision.Apr 7 2018, 10:30 PM
This revision is now accepted and ready to land.Apr 7 2018, 10:30 PM
Closed by commit rP467343: biology/tabixpp: C++ wrapper to tabix indexer (authored by jwb). · Explain WhyApr 14 2018, 11:52 PM
This revision was automatically updated to reflect the committed changes.

Revision Contents
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Diff 41145

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biology/Makefile

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biology/tabixpp/

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biology/tabixpp/Makefile

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biology/tabixpp/distinfo

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biology/tabixpp/files/

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biology/tabixpp/files/Makefile

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biology/tabixpp/pkg-descr

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