epacts: Fix build (Add R bl3)

[Jason Bacon <bacon4000%gmail.com@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Thu Aug 31 16:04:34 2017 -0500
Changeset:	e127101527d27df235baefe5e1f612f8dd68a9f6

Modified Files:
	epacts/Makefile
	epacts/PLIST

Log Message:
epacts: Fix build (Add R bl3)

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=e127101527d27df235baefe5e1f612f8dd68a9f6

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 epacts/Makefile |  9 ++-------
 epacts/PLIST    | 38 +++++++++++++++++++++++++++++++++++++-
 2 files changed, 39 insertions(+), 8 deletions(-)

diffs:
diff --git a/epacts/Makefile b/epacts/Makefile
index 78a6e9cf52..6ded8f35c9 100644
--- a/epacts/Makefile
+++ b/epacts/Makefile
@@ -19,11 +19,7 @@ COMMENT=	Efficient and Parallelizable Association Container Toolbox
 # Check this
 LICENSE=	gnu-gpl-v3
 
-# Test and change if necessary.
-# MAKE_JOBS_SAFE=	no
-
 DEPENDS+=	gnuplot>=0:../../graphics/gnuplot
-DEPENDS+=	R>=0:../../math/R
 
 # Just assuming C and C++: Adjust this!
 USE_LANGUAGES=	c c++
@@ -42,11 +38,10 @@ pre-configure:
 	cd ${WRKSRC} && autoreconf -if
 
 post-install:
-	${STRIP_CMD} \
+	${STRIP} \
 		${DESTDIR}${PREFIX}/lib/mmSKAT/libs/mmSKAT.so \
 		${DESTDIR}${PREFIX}/lib/epactsR/libs/epactsR.so
 
-# Convert any _DEPENDS above that have a buildlink3.mk
-# .include "../..///buildlink3.mk"
+.include "../../math/R/buildlink3.mk"
 .include "../../devel/zlib/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/epacts/PLIST b/epacts/PLIST
index b02d41c173..c604b7fd18 100644
--- a/epacts/PLIST
+++ b/epacts/PLIST
@@ -23,6 +23,43 @@ bin/tabix
 bin/test_run_epacts.sh
 bin/vcfast
 bin/wGetOptions.pm
+lib/epactsR/DESCRIPTION
+lib/epactsR/Meta/Rd.rds
+lib/epactsR/Meta/hsearch.rds
+lib/epactsR/Meta/links.rds
+lib/epactsR/Meta/nsInfo.rds
+lib/epactsR/Meta/package.rds
+lib/epactsR/NAMESPACE
+lib/epactsR/help/AnIndex
+lib/epactsR/help/aliases.rds
+lib/epactsR/help/epactsR.rdb
+lib/epactsR/help/epactsR.rdx
+lib/epactsR/help/paths.rds
+lib/epactsR/html/00Index.html
+lib/epactsR/html/R.css
+lib/epactsR/libs/epactsR.so
+lib/mmSKAT/DESCRIPTION
+lib/mmSKAT/Meta/Rd.rds
+lib/mmSKAT/Meta/data.rds
+lib/mmSKAT/Meta/hsearch.rds
+lib/mmSKAT/Meta/links.rds
+lib/mmSKAT/Meta/nsInfo.rds
+lib/mmSKAT/Meta/package.rds
+lib/mmSKAT/NAMESPACE
+lib/mmSKAT/R/mmSKAT
+lib/mmSKAT/R/mmSKAT.rdb
+lib/mmSKAT/R/mmSKAT.rdx
+lib/mmSKAT/data/SKAT.example.rda
+lib/mmSKAT/data/SKAT.haplotypes.rda
+lib/mmSKAT/data/datalist
+lib/mmSKAT/help/AnIndex
+lib/mmSKAT/help/aliases.rds
+lib/mmSKAT/help/mmSKAT.rdb
+lib/mmSKAT/help/mmSKAT.rdx
+lib/mmSKAT/help/paths.rds
+lib/mmSKAT/html/00Index.html
+lib/mmSKAT/html/R.css
+lib/mmSKAT/libs/mmSKAT.so
 share/EPACTS/1000G_dummy_pheno.ped
 share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz
 share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz.tbi
@@ -84,4 +121,3 @@ share/EPACTS/wgEncodeBroadHmmNhekHMM.bed.gz
 share/EPACTS/wgEncodeBroadHmmNhekHMM.bed.gz.tbi
 share/EPACTS/wgEncodeBroadHmmNhlfHMM.bed.gz
 share/EPACTS/wgEncodeBroadHmmNhlfHMM.bed.gz.tbi
-@pkgdir lib