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subread: Successful build on CentOS, generate PLIST

Module Name:	pkgsrc-wip
Committed By:	Jason W Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Tue Mar 30 13:49:28 2021 -0500
Changeset:	dfe6a01a8ac29fca37d91bf38845e61f6222901c

Modified Files:
	subread/Makefile
	subread/PLIST
	subread/distinfo
	subread/files/Makefile.pkg
	subread/patches/patch-HelperFunctions.c
	subread/patches/patch-core-junction.c
	subread/patches/patch-gene-algorithms.c
	subread/patches/patch-input-files.c
	subread/patches/patch-long-hashtable.c
	subread/patches/patch-longread-one_LRMsorted-hashtable.c
	subread/patches/patch-longread-one_Makefile
	subread/patches/patch-longread-one_longread-mapping.c
	subread/patches/patch-read-repair.c
	subread/patches/patch-sambam-file.c
	subread/patches/patch-sorted-hashtable.c
	subread/patches/patch-subread.h

Log Message:
subread: Successful build on CentOS, generate PLIST

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=dfe6a01a8ac29fca37d91bf38845e61f6222901c

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

diffstat:
 subread/Makefile                                   |  3 +--
 subread/PLIST                                      | 16 +++++++++++++++
 subread/distinfo                                   | 24 +++++++++++-----------
 subread/files/Makefile.pkg                         |  2 +-
 subread/patches/patch-HelperFunctions.c            |  2 ++
 subread/patches/patch-core-junction.c              |  2 ++
 subread/patches/patch-gene-algorithms.c            |  2 ++
 subread/patches/patch-input-files.c                |  2 ++
 subread/patches/patch-long-hashtable.c             |  2 ++
 .../patch-longread-one_LRMsorted-hashtable.c       |  2 ++
 subread/patches/patch-longread-one_Makefile        |  2 ++
 .../patches/patch-longread-one_longread-mapping.c  |  2 ++
 subread/patches/patch-read-repair.c                |  2 ++
 subread/patches/patch-sambam-file.c                |  1 -
 subread/patches/patch-sorted-hashtable.c           |  2 ++
 subread/patches/patch-subread.h                    |  2 ++
 16 files changed, 52 insertions(+), 16 deletions(-)

diffs:
diff --git a/subread/Makefile b/subread/Makefile
index 25a07c28af..b2b9da8d4d 100644
--- a/subread/Makefile
+++ b/subread/Makefile
@@ -28,6 +28,5 @@ INSTALL_TARGET=	install-strip
 
 # Convert any _DEPENDS above that have a buildlink3.mk
 # .include "../..///buildlink3.mk"
-# CentOS doesn't have zlib in the base, so uncomment if needed.
-# .include "../../devel/zlib/buildlink3.mk"
+.include "../../devel/zlib/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/subread/PLIST b/subread/PLIST
index 48d96a5493..685392aaee 100644
--- a/subread/PLIST
+++ b/subread/PLIST
@@ -1 +1,17 @@
 @comment $NetBSD$
+bin/detectionCall
+bin/exactSNP
+bin/featureCounts
+bin/flattenGTF
+bin/genRandomReads
+bin/propmapped
+bin/qualityScores
+bin/removeDup
+bin/repair
+bin/subindel
+bin/subjunc
+bin/sublong
+bin/subread-align
+bin/subread-buildindex
+bin/subread-fullscan
+bin/txUnique
diff --git a/subread/distinfo b/subread/distinfo
index 2304991298..396c4efbbe 100644
--- a/subread/distinfo
+++ b/subread/distinfo
@@ -4,15 +4,15 @@ SHA1 (subread-2.0.2-source.tar.gz) = 1f5eb1ffa0184e21321fb9e40a9f02dd94bb19ff
 RMD160 (subread-2.0.2-source.tar.gz) = 2cfa127a7bea963d67330edee2ca226f9d6dde49
 SHA512 (subread-2.0.2-source.tar.gz) = 549164aadcd1e05cd1f941a4c10d6e19f904d2d75dae8391bbf3003a26e13f6a14cc22618662c2baf804b4d020a58e7ba0b0be9b4ff1181ad981a24270ffb64e
 Size (subread-2.0.2-source.tar.gz) = 23295764 bytes
-SHA1 (patch-HelperFunctions.c) = b1205dfe8c57a9033237086e39ffa8e362595bf2
-SHA1 (patch-core-junction.c) = 39b7acbc4a61c40c112c8451ab234bb06d189462
-SHA1 (patch-gene-algorithms.c) = e8f4f0e5747cba279bf8fb88a0743a58065cf7a4
-SHA1 (patch-input-files.c) = cd85b2df930eba3f910c534d93933bf4f4355cd3
-SHA1 (patch-long-hashtable.c) = c6d6fef3c6925e94d7267db23dcba97aa5ad71a3
-SHA1 (patch-longread-one_LRMsorted-hashtable.c) = 956bc03d1ce3e820a61b81bd2d524916a33e0bce
-SHA1 (patch-longread-one_Makefile) = aae55c436af25e5513e79f4dcd6aee03d2dc48d2
-SHA1 (patch-longread-one_longread-mapping.c) = 9179704c5fc3dda691e8d13e08bb5dbe66f93e44
-SHA1 (patch-read-repair.c) = 848fd626695cbe494b2579d7f18d6b5381986811
-SHA1 (patch-sambam-file.c) = 6c6edfbefcffece7c5e296e8224884f6ac34445d
-SHA1 (patch-sorted-hashtable.c) = 68cbf2b4cc516d825ccdd4260d7b2a38e9e4dd3c
-SHA1 (patch-subread.h) = f259b8dfd4d3394f4dbeee5ab5c3ac4f6bb76308
+SHA1 (patch-HelperFunctions.c) = e46a1020b9106c79f5dcabb4594c75b7479e2dff
+SHA1 (patch-core-junction.c) = 481cd069aa42d673bbc10c80bb9548547e808b0c
+SHA1 (patch-gene-algorithms.c) = 19d3c0ad564175b413ebbeb513bd6332c9409daf
+SHA1 (patch-input-files.c) = 49a695b02d3fe37c66001cb728a282f588f795ab
+SHA1 (patch-long-hashtable.c) = 3180660daf6ed94a785f47972c117370ce310ef5
+SHA1 (patch-longread-one_LRMsorted-hashtable.c) = f08066fab9cb83da77a289b269395693ab80393a
+SHA1 (patch-longread-one_Makefile) = 48e06a0d3987aa47aefa17fcfdb395f647bc4141
+SHA1 (patch-longread-one_longread-mapping.c) = c82876cdb1186eba2afd9b684a58c8013d0143bb
+SHA1 (patch-read-repair.c) = 4d7085ec8558647c7d92f5d0697b04b526496a75
+SHA1 (patch-sambam-file.c) = 007489e7140c8e22116a0748b734c636adc40896
+SHA1 (patch-sorted-hashtable.c) = 691dc605c2c5451eb7857366df4386de9813bace
+SHA1 (patch-subread.h) = 182016760358f56a845cdf49899a5c7ccfe84aef
diff --git a/subread/files/Makefile.pkg b/subread/files/Makefile.pkg
index 2ae783e699..e6686df442 100644
--- a/subread/files/Makefile.pkg
+++ b/subread/files/Makefile.pkg
@@ -4,7 +4,7 @@ include makefile.version
 
 CCFLAGS = -DMAKE_FOR_EXON  -DMAKE_STANDALONE \
 	-DSUBREAD_VERSION=\"${SUBREAD_VERSION}\"  -D_FILE_OFFSET_BITS=64
-LDFLAGS += -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm
+LDFLAGS += -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lz -lm
 CC ?= gcc
 CC += ${CCFLAGS}
 
diff --git a/subread/patches/patch-HelperFunctions.c b/subread/patches/patch-HelperFunctions.c
index 201347784d..9d269bdb53 100644
--- a/subread/patches/patch-HelperFunctions.c
+++ b/subread/patches/patch-HelperFunctions.c
@@ -1,5 +1,7 @@
 $NetBSD$
 
+# Use predefined macros
+
 --- HelperFunctions.c.orig	2020-06-04 23:58:40 UTC
 +++ HelperFunctions.c
 @@ -845,7 +845,7 @@ int strcmp_number(char * s1, char * s2)
diff --git a/subread/patches/patch-core-junction.c b/subread/patches/patch-core-junction.c
index fef3248934..408f848df7 100644
--- a/subread/patches/patch-core-junction.c
+++ b/subread/patches/patch-core-junction.c
@@ -1,5 +1,7 @@
 $NetBSD$
 
+# Portability
+
 --- core-junction.c.orig	2018-11-08 15:19:02 UTC
 +++ core-junction.c
 @@ -22,6 +22,7 @@
diff --git a/subread/patches/patch-gene-algorithms.c b/subread/patches/patch-gene-algorithms.c
index 10d02f179d..9b6ab3427c 100644
--- a/subread/patches/patch-gene-algorithms.c
+++ b/subread/patches/patch-gene-algorithms.c
@@ -1,5 +1,7 @@
 $NetBSD$
 
+# Use prefefined macros
+
 --- gene-algorithms.c.orig	2021-03-30 13:51:05 UTC
 +++ gene-algorithms.c
 @@ -29,7 +29,7 @@
diff --git a/subread/patches/patch-input-files.c b/subread/patches/patch-input-files.c
index 823b842c13..21d0b7ec66 100644
--- a/subread/patches/patch-input-files.c
+++ b/subread/patches/patch-input-files.c
@@ -1,5 +1,7 @@
 $NetBSD$
 
+# Use predefined macros
+
 --- input-files.c.orig	2020-06-05 00:33:03 UTC
 +++ input-files.c
 @@ -48,7 +48,7 @@ FILE * f_subr_open(const char * fname, const char * mo
diff --git a/subread/patches/patch-long-hashtable.c b/subread/patches/patch-long-hashtable.c
index 9139fa87e1..957b778b72 100644
--- a/subread/patches/patch-long-hashtable.c
+++ b/subread/patches/patch-long-hashtable.c
@@ -1,5 +1,7 @@
 $NetBSD$
 
+# Use predefined macros
+
 --- long-hashtable.c.orig	2020-06-04 23:59:33 UTC
 +++ long-hashtable.c
 @@ -22,7 +22,7 @@
diff --git a/subread/patches/patch-longread-one_LRMsorted-hashtable.c b/subread/patches/patch-longread-one_LRMsorted-hashtable.c
index ecce900e7c..08486388ec 100644
--- a/subread/patches/patch-longread-one_LRMsorted-hashtable.c
+++ b/subread/patches/patch-longread-one_LRMsorted-hashtable.c
@@ -1,5 +1,7 @@
 $NetBSD$
 
+# Use predefined macros
+
 --- longread-one/LRMsorted-hashtable.c.orig	2018-11-08 14:47:43 UTC
 +++ longread-one/LRMsorted-hashtable.c
 @@ -22,11 +22,9 @@
diff --git a/subread/patches/patch-longread-one_Makefile b/subread/patches/patch-longread-one_Makefile
index 7feb65ace2..3ef12e5c27 100644
--- a/subread/patches/patch-longread-one_Makefile
+++ b/subread/patches/patch-longread-one_Makefile
@@ -1,5 +1,7 @@
 $NetBSD$
 
+# Respect env
+
 --- longread-one/Makefile.orig	2019-09-04 04:22:49 UTC
 +++ longread-one/Makefile
 @@ -1,12 +1,12 @@
diff --git a/subread/patches/patch-longread-one_longread-mapping.c b/subread/patches/patch-longread-one_longread-mapping.c
index 40d4b6c740..49de12641e 100644
--- a/subread/patches/patch-longread-one_longread-mapping.c
+++ b/subread/patches/patch-longread-one_longread-mapping.c
@@ -1,5 +1,7 @@
 $NetBSD$
 
+# Use predefined macros and gettimeofday()
+
 --- longread-one/longread-mapping.c.orig	2021-03-30 13:58:29 UTC
 +++ longread-one/longread-mapping.c
 @@ -30,7 +30,9 @@
diff --git a/subread/patches/patch-read-repair.c b/subread/patches/patch-read-repair.c
index 77210ad03b..df2dbf8afb 100644
--- a/subread/patches/patch-read-repair.c
+++ b/subread/patches/patch-read-repair.c
@@ -1,5 +1,7 @@
 $NetBSD$
 
+# Portability
+
 --- read-repair.c.orig	2018-11-08 15:20:06 UTC
 +++ read-repair.c
 @@ -3,6 +3,7 @@
diff --git a/subread/patches/patch-sambam-file.c b/subread/patches/patch-sambam-file.c
index b53a634b58..a3cddf1959 100644
--- a/subread/patches/patch-sambam-file.c
+++ b/subread/patches/patch-sambam-file.c
@@ -2,7 +2,6 @@ $NetBSD$
 
 # Portability
 
---- sambam-file.c.orig	2018-11-08 15:20:35 UTC
 --- sambam-file.c.orig	2021-03-27 07:38:08.000000000 +0000
 +++ sambam-file.c
 @@ -30,6 +30,7 @@
diff --git a/subread/patches/patch-sorted-hashtable.c b/subread/patches/patch-sorted-hashtable.c
index 104dc22335..a61e58cb77 100644
--- a/subread/patches/patch-sorted-hashtable.c
+++ b/subread/patches/patch-sorted-hashtable.c
@@ -1,5 +1,7 @@
 $NetBSD$
 
+# Portability
+
 --- sorted-hashtable.c.orig	2018-11-08 03:33:50 UTC
 +++ sorted-hashtable.c
 @@ -23,11 +23,9 @@
diff --git a/subread/patches/patch-subread.h b/subread/patches/patch-subread.h
index 40f91694a8..c5e179bfab 100644
--- a/subread/patches/patch-subread.h
+++ b/subread/patches/patch-subread.h
@@ -1,5 +1,7 @@
 $NetBSD$
 
+# Use predefined macros
+
 --- subread.h.orig	2018-11-08 14:46:06 UTC
 +++ subread.h
 @@ -102,7 +102,7 @@
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