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*/*: sync with upstream
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Taken from: HardenedBSD
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@fichtner
fichtner committed May 21, 2018
1 parent 3bcf8ab commit e45be81
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Showing 127 changed files with 1,987 additions and 1,533 deletions.
4 changes: 2 additions & 2 deletions archivers/zopfli/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@

PORTNAME= zopfli
DISTVERSIONPREFIX= ${PORTNAME}-
DISTVERSION= 1.0.1
DISTVERSION= 1.0.2
CATEGORIES= archivers

MAINTAINER= [email protected]
Expand Down Expand Up @@ -31,7 +31,7 @@ do-install:
.for f in ${PORTNAME} ${PORTNAME}png
${INSTALL_PROGRAM} ${WRKSRC}/${f} ${STAGEDIR}${PREFIX}/bin
.endfor
.for f in lib${PORTNAME}.so.1.0.1 lib${PORTNAME}png.so.1.0.0
.for f in lib${PORTNAME}.so.1.0.2 lib${PORTNAME}png.so.1.0.2
${INSTALL_LIB} ${WRKSRC}/${f} ${STAGEDIR}${PREFIX}/lib
${LN} -fs ${f} ${STAGEDIR}${PREFIX}/lib/${f:R:R}
${LN} -fs ${f:R:R} ${STAGEDIR}${PREFIX}/lib/${f:R:R:R}
Expand Down
5 changes: 3 additions & 2 deletions archivers/zopfli/distinfo
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Original file line number Diff line number Diff line change
@@ -1,2 +1,3 @@
SHA256 (google-zopfli-zopfli-1.0.1_GH0.tar.gz) = 29743d727a4e0ecd1b93e0bf89476ceeb662e809ab2e6ab007a0b0344800e9b4
SIZE (google-zopfli-zopfli-1.0.1_GH0.tar.gz) = 128178
TIMESTAMP = 1526822287
SHA256 (google-zopfli-zopfli-1.0.2_GH0.tar.gz) = 4a570307c37172d894ec4ef93b6e8e3aacc401e78cbcc51cf85b212dbc379a55
SIZE (google-zopfli-zopfli-1.0.2_GH0.tar.gz) = 136035
5 changes: 3 additions & 2 deletions archivers/zopfli/pkg-plist
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@ include/zopfli/hash.h
include/zopfli/katajainen.h
include/zopfli/lz77.h
include/zopfli/squeeze.h
include/zopfli/symbols.h
include/zopfli/tree.h
include/zopfli/util.h
include/zopfli/zlib_container.h
Expand All @@ -17,7 +18,7 @@ include/zopflipng/lodepng/lodepng_util.h
include/zopflipng/zopflipng_lib.h
lib/libzopfli.so
lib/libzopfli.so.1
lib/libzopfli.so.1.0.1
lib/libzopfli.so.1.0.2
lib/libzopflipng.so
lib/libzopflipng.so.1
lib/libzopflipng.so.1.0.0
lib/libzopflipng.so.1.0.2
7 changes: 4 additions & 3 deletions biology/clustalw/Makefile
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Expand Up @@ -3,15 +3,16 @@

PORTNAME= clustalw
PORTVERSION= 2.1
PORTREVISION= 1
PORTREVISION= 2
CATEGORIES= biology
MASTER_SITES= ftp://ftp.ebi.ac.uk/pub/software/clustalw2/${PORTVERSION}/ \
http://www.clustal.org/download/${PORTVERSION}/

MAINTAINER= ports@FreeBSD.org
MAINTAINER= jwb@FreeBSD.org
COMMENT= Multiple alignment program for DNA or proteins

RESTRICTED= No commercial use.
LICENSE= LGPL3
LICENSE_FILE= ${WRKSRC}/COPYING

GNU_CONFIGURE= yes

Expand Down
4 changes: 2 additions & 2 deletions biology/clustalw/files/patch-src-general-VectorOutOfRange.h
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
--- src/general/VectorOutOfRange.h.orig 2013-12-20 23:16:13.000000000 +0800
+++ src/general/VectorOutOfRange.h 2013-12-20 23:16:37.000000000 +0800
--- src/general/VectorOutOfRange.h.orig 2010-09-09 14:26:01 UTC
+++ src/general/VectorOutOfRange.h
@@ -5,6 +5,7 @@
*/
#include <stdexcept>
Expand Down
4 changes: 1 addition & 3 deletions biology/molden/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@

PORTNAME= molden
PORTVERSION= 5.7
PORTREVISION= 14
PORTREVISION= 15
PORTEPOCH= 1
CATEGORIES= biology
MASTER_SITES= ftp://ftp.cmbi.ru.nl/pub/molgraph/molden/
Expand All @@ -17,8 +17,6 @@ LICENSE_NAME= Molden
LICENSE_FILE= ${WRKSRC}/CopyRight
LICENSE_PERMS= auto-accept

BROKEN= checksum and size mismatch

RESTRICTED= free for academic, non profit usage; do not re-distribute source and executable.

WRKSRC= ${WRKDIR}/${PORTNAME}${PORTVERSION}
Expand Down
6 changes: 3 additions & 3 deletions biology/molden/distinfo
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Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
TIMESTAMP = 1509238230
SHA256 (molden5.7.tar.gz) = 1ab88d4c6bfb617da6b9ce84a02f3427eeded2ee3bbbb769115d25505f08583d
SIZE (molden5.7.tar.gz) = 5346266
TIMESTAMP = 1526851227
SHA256 (molden5.7.tar.gz) = 10e3c02b63e6aa277922488f48be1bbd231e5bb111fb86fa162293a6fbc9718a
SIZE (molden5.7.tar.gz) = 5346379
10 changes: 9 additions & 1 deletion databases/mongodb32/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@

PORTNAME= mongodb32
PORTVERSION= 3.2.11
PORTREVISION= 1
PORTREVISION= 2
DISTVERSIONPREFIX= r
CATEGORIES= databases net
MASTER_SITES= https://fastdl.mongodb.org/src/ \
Expand Down Expand Up @@ -51,6 +51,14 @@ GROUPS= mongodb

USE_RC_SUBR= mongod

.include <bsd.port.options.mk>

.if ${OPSYS} == FreeBSD && ${OSVERSION} >= 1200057
SUB_LIST+= LEGACY_LIMITS="@comment " MODERN_LIMITS=""
.else
SUB_LIST+= LEGACY_LIMITS="" MODERN_LIMITS="@comment "
.endif

ALL_TARGET= core
TEST_TARGET= unittests

Expand Down
21 changes: 11 additions & 10 deletions databases/mongodb32/files/mongod.in
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Original file line number Diff line number Diff line change
Expand Up @@ -7,11 +7,11 @@
# Add the following lines to /etc/rc.conf.local or /etc/rc.conf
# to enable this service:
#
# mongod_enable (bool): Set to "NO" by default.
# mongod_enable (bool): Set to "NO" by default.
# Set it to "YES" to enable mongod.
# mongod_limits (bool): Set to "NO" by default.
# Set it to yes to run `limits -e -U mongodb`
# just before mongod starts.
%%LEGACY_LIMITS%%# mongod_limits (bool): Set to "NO" by default.
%%LEGACY_LIMITS%%# Set it to yes to run `limits -e -U mongodb`
%%LEGACY_LIMITS%%# just before mongod starts.
# mongod_dbpath (str): Default to "/var/db/mongodb"
# Base database directory.
# mongod_flags (str): Custom additional arguments to be passed to mongod.
Expand All @@ -28,7 +28,7 @@ rcvar=mongod_enable
load_rc_config $name

: ${mongod_enable="NO"}
: ${mongod_limits="NO"}
%%LEGACY_LIMITS%%: ${mongod_limits="NO"}
: ${mongod_dbpath="/var/db/mongodb"}
: ${mongod_flags="--logpath ${mongod_dbpath}/mongod.log --logappend"}
: ${mongod_user="mongodb"}
Expand All @@ -52,11 +52,12 @@ mongod_prestart()
if [ ! -d ${mongod_dbpath} ]; then
mongod_create_dbpath || return 1
fi
if checkyesno mongod_limits; then
eval `/usr/bin/limits -e -U ${mongod_user}` 2>/dev/null
else
return 0
fi
%%LEGACY_LIMITS%% if checkyesno mongod_limits; then
%%LEGACY_LIMITS%% eval `/usr/bin/limits -e -U ${mongod_user}` 2>/dev/null
%%LEGACY_LIMITS%% else
%%LEGACY_LIMITS%% return 0
%%LEGACY_LIMITS%% fi
%%MODERN_LIMITS%% return 0
}

run_rc_command "$1"
4 changes: 1 addition & 3 deletions devel/flang-clang/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
# $FreeBSD$

PORTNAME= flang-clang
DISTVERSION= 5.0-20180112
DISTVERSION= 5.0-20180506
PORTREVISION= 0
CATEGORIES= devel lang

Expand All @@ -14,8 +14,6 @@ LICENSE_NAME= LLVM Release License
LICENSE_FILE= ${WRKSRC}/LICENSE.TXT
LICENSE_PERMS= dist-mirror dist-sell pkg-mirror pkg-sell auto-accept

BROKEN= fails to package

BUILD_DEPENDS= llvm50>=0:devel/llvm50
RUN_DEPENDS= llvm50>=0:devel/llvm50

Expand Down
6 changes: 3 additions & 3 deletions devel/flang-clang/distinfo
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Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
TIMESTAMP = 1515770420
SHA256 (flang-compiler-clang-5.0-20180112-64043d5_GH0.tar.gz) = 63f3b010bb90131099fe5f57e09e50e39aff37a1ac76fb0d1bb8d0ed7bf9e295
SIZE (flang-compiler-clang-5.0-20180112-64043d5_GH0.tar.gz) = 16002999
TIMESTAMP = 1525637486
SHA256 (flang-compiler-clang-5.0-20180506-64043d5_GH0.tar.gz) = 63f3b010bb90131099fe5f57e09e50e39aff37a1ac76fb0d1bb8d0ed7bf9e295
SIZE (flang-compiler-clang-5.0-20180506-64043d5_GH0.tar.gz) = 16002999
192 changes: 96 additions & 96 deletions devel/flang-clang/pkg-plist
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Expand Up @@ -502,102 +502,102 @@ flang/include/clang/Tooling/Refactoring/Rename/USRLocFinder.h
flang/include/clang/Tooling/RefactoringCallbacks.h
flang/include/clang/Tooling/ReplacementsYaml.h
flang/include/clang/Tooling/Tooling.h
flang/lib/clang/5.0.1/include/__clang_cuda_builtin_vars.h
flang/lib/clang/5.0.1/include/__clang_cuda_cmath.h
flang/lib/clang/5.0.1/include/__clang_cuda_complex_builtins.h
flang/lib/clang/5.0.1/include/__clang_cuda_intrinsics.h
flang/lib/clang/5.0.1/include/__clang_cuda_math_forward_declares.h
flang/lib/clang/5.0.1/include/__clang_cuda_runtime_wrapper.h
flang/lib/clang/5.0.1/include/__stddef_max_align_t.h
flang/lib/clang/5.0.1/include/__wmmintrin_aes.h
flang/lib/clang/5.0.1/include/__wmmintrin_pclmul.h
flang/lib/clang/5.0.1/include/adxintrin.h
flang/lib/clang/5.0.1/include/altivec.h
flang/lib/clang/5.0.1/include/ammintrin.h
flang/lib/clang/5.0.1/include/arm_acle.h
flang/lib/clang/5.0.1/include/arm_neon.h
flang/lib/clang/5.0.1/include/armintr.h
flang/lib/clang/5.0.1/include/avx2intrin.h
flang/lib/clang/5.0.1/include/avx512bwintrin.h
flang/lib/clang/5.0.1/include/avx512cdintrin.h
flang/lib/clang/5.0.1/include/avx512dqintrin.h
flang/lib/clang/5.0.1/include/avx512erintrin.h
flang/lib/clang/5.0.1/include/avx512fintrin.h
flang/lib/clang/5.0.1/include/avx512ifmaintrin.h
flang/lib/clang/5.0.1/include/avx512ifmavlintrin.h
flang/lib/clang/5.0.1/include/avx512pfintrin.h
flang/lib/clang/5.0.1/include/avx512vbmiintrin.h
flang/lib/clang/5.0.1/include/avx512vbmivlintrin.h
flang/lib/clang/5.0.1/include/avx512vlbwintrin.h
flang/lib/clang/5.0.1/include/avx512vlcdintrin.h
flang/lib/clang/5.0.1/include/avx512vldqintrin.h
flang/lib/clang/5.0.1/include/avx512vlintrin.h
flang/lib/clang/5.0.1/include/avx512vpopcntdqintrin.h
flang/lib/clang/5.0.1/include/avxintrin.h
flang/lib/clang/5.0.1/include/bmi2intrin.h
flang/lib/clang/5.0.1/include/bmiintrin.h
flang/lib/clang/5.0.1/include/clflushoptintrin.h
flang/lib/clang/5.0.1/include/clzerointrin.h
flang/lib/clang/5.0.1/include/cpuid.h
flang/lib/clang/5.0.1/include/cuda_wrappers/algorithm
flang/lib/clang/5.0.1/include/cuda_wrappers/complex
flang/lib/clang/5.0.1/include/cuda_wrappers/new
flang/lib/clang/5.0.1/include/emmintrin.h
flang/lib/clang/5.0.1/include/f16cintrin.h
flang/lib/clang/5.0.1/include/float.h
flang/lib/clang/5.0.1/include/fma4intrin.h
flang/lib/clang/5.0.1/include/fmaintrin.h
flang/lib/clang/5.0.1/include/fxsrintrin.h
flang/lib/clang/5.0.1/include/htmintrin.h
flang/lib/clang/5.0.1/include/htmxlintrin.h
flang/lib/clang/5.0.1/include/ia32intrin.h
flang/lib/clang/5.0.1/include/immintrin.h
flang/lib/clang/5.0.1/include/intrin.h
flang/lib/clang/5.0.1/include/inttypes.h
flang/lib/clang/5.0.1/include/iso646.h
flang/lib/clang/5.0.1/include/limits.h
flang/lib/clang/5.0.1/include/lwpintrin.h
flang/lib/clang/5.0.1/include/lzcntintrin.h
flang/lib/clang/5.0.1/include/mm3dnow.h
flang/lib/clang/5.0.1/include/mm_malloc.h
flang/lib/clang/5.0.1/include/mmintrin.h
flang/lib/clang/5.0.1/include/module.modulemap
flang/lib/clang/5.0.1/include/msa.h
flang/lib/clang/5.0.1/include/mwaitxintrin.h
flang/lib/clang/5.0.1/include/nmmintrin.h
flang/lib/clang/5.0.1/include/opencl-c.h
flang/lib/clang/5.0.1/include/pkuintrin.h
flang/lib/clang/5.0.1/include/pmmintrin.h
flang/lib/clang/5.0.1/include/popcntintrin.h
flang/lib/clang/5.0.1/include/prfchwintrin.h
flang/lib/clang/5.0.1/include/rdseedintrin.h
flang/lib/clang/5.0.1/include/rtmintrin.h
flang/lib/clang/5.0.1/include/s390intrin.h
flang/lib/clang/5.0.1/include/shaintrin.h
flang/lib/clang/5.0.1/include/smmintrin.h
flang/lib/clang/5.0.1/include/stdalign.h
flang/lib/clang/5.0.1/include/stdarg.h
flang/lib/clang/5.0.1/include/stdatomic.h
flang/lib/clang/5.0.1/include/stdbool.h
flang/lib/clang/5.0.1/include/stddef.h
flang/lib/clang/5.0.1/include/stdint.h
flang/lib/clang/5.0.1/include/stdnoreturn.h
flang/lib/clang/5.0.1/include/tbmintrin.h
flang/lib/clang/5.0.1/include/tgmath.h
flang/lib/clang/5.0.1/include/tmmintrin.h
flang/lib/clang/5.0.1/include/unwind.h
flang/lib/clang/5.0.1/include/vadefs.h
flang/lib/clang/5.0.1/include/varargs.h
flang/lib/clang/5.0.1/include/vecintrin.h
flang/lib/clang/5.0.1/include/wmmintrin.h
flang/lib/clang/5.0.1/include/x86intrin.h
flang/lib/clang/5.0.1/include/xmmintrin.h
flang/lib/clang/5.0.1/include/xopintrin.h
flang/lib/clang/5.0.1/include/xsavecintrin.h
flang/lib/clang/5.0.1/include/xsaveintrin.h
flang/lib/clang/5.0.1/include/xsaveoptintrin.h
flang/lib/clang/5.0.1/include/xsavesintrin.h
flang/lib/clang/5.0.1/include/xtestintrin.h
flang/lib/clang/5.0.2/include/__clang_cuda_builtin_vars.h
flang/lib/clang/5.0.2/include/__clang_cuda_cmath.h
flang/lib/clang/5.0.2/include/__clang_cuda_complex_builtins.h
flang/lib/clang/5.0.2/include/__clang_cuda_intrinsics.h
flang/lib/clang/5.0.2/include/__clang_cuda_math_forward_declares.h
flang/lib/clang/5.0.2/include/__clang_cuda_runtime_wrapper.h
flang/lib/clang/5.0.2/include/__stddef_max_align_t.h
flang/lib/clang/5.0.2/include/__wmmintrin_aes.h
flang/lib/clang/5.0.2/include/__wmmintrin_pclmul.h
flang/lib/clang/5.0.2/include/adxintrin.h
flang/lib/clang/5.0.2/include/altivec.h
flang/lib/clang/5.0.2/include/ammintrin.h
flang/lib/clang/5.0.2/include/arm_acle.h
flang/lib/clang/5.0.2/include/arm_neon.h
flang/lib/clang/5.0.2/include/armintr.h
flang/lib/clang/5.0.2/include/avx2intrin.h
flang/lib/clang/5.0.2/include/avx512bwintrin.h
flang/lib/clang/5.0.2/include/avx512cdintrin.h
flang/lib/clang/5.0.2/include/avx512dqintrin.h
flang/lib/clang/5.0.2/include/avx512erintrin.h
flang/lib/clang/5.0.2/include/avx512fintrin.h
flang/lib/clang/5.0.2/include/avx512ifmaintrin.h
flang/lib/clang/5.0.2/include/avx512ifmavlintrin.h
flang/lib/clang/5.0.2/include/avx512pfintrin.h
flang/lib/clang/5.0.2/include/avx512vbmiintrin.h
flang/lib/clang/5.0.2/include/avx512vbmivlintrin.h
flang/lib/clang/5.0.2/include/avx512vlbwintrin.h
flang/lib/clang/5.0.2/include/avx512vlcdintrin.h
flang/lib/clang/5.0.2/include/avx512vldqintrin.h
flang/lib/clang/5.0.2/include/avx512vlintrin.h
flang/lib/clang/5.0.2/include/avx512vpopcntdqintrin.h
flang/lib/clang/5.0.2/include/avxintrin.h
flang/lib/clang/5.0.2/include/bmi2intrin.h
flang/lib/clang/5.0.2/include/bmiintrin.h
flang/lib/clang/5.0.2/include/clflushoptintrin.h
flang/lib/clang/5.0.2/include/clzerointrin.h
flang/lib/clang/5.0.2/include/cpuid.h
flang/lib/clang/5.0.2/include/cuda_wrappers/algorithm
flang/lib/clang/5.0.2/include/cuda_wrappers/complex
flang/lib/clang/5.0.2/include/cuda_wrappers/new
flang/lib/clang/5.0.2/include/emmintrin.h
flang/lib/clang/5.0.2/include/f16cintrin.h
flang/lib/clang/5.0.2/include/float.h
flang/lib/clang/5.0.2/include/fma4intrin.h
flang/lib/clang/5.0.2/include/fmaintrin.h
flang/lib/clang/5.0.2/include/fxsrintrin.h
flang/lib/clang/5.0.2/include/htmintrin.h
flang/lib/clang/5.0.2/include/htmxlintrin.h
flang/lib/clang/5.0.2/include/ia32intrin.h
flang/lib/clang/5.0.2/include/immintrin.h
flang/lib/clang/5.0.2/include/intrin.h
flang/lib/clang/5.0.2/include/inttypes.h
flang/lib/clang/5.0.2/include/iso646.h
flang/lib/clang/5.0.2/include/limits.h
flang/lib/clang/5.0.2/include/lwpintrin.h
flang/lib/clang/5.0.2/include/lzcntintrin.h
flang/lib/clang/5.0.2/include/mm3dnow.h
flang/lib/clang/5.0.2/include/mm_malloc.h
flang/lib/clang/5.0.2/include/mmintrin.h
flang/lib/clang/5.0.2/include/module.modulemap
flang/lib/clang/5.0.2/include/msa.h
flang/lib/clang/5.0.2/include/mwaitxintrin.h
flang/lib/clang/5.0.2/include/nmmintrin.h
flang/lib/clang/5.0.2/include/opencl-c.h
flang/lib/clang/5.0.2/include/pkuintrin.h
flang/lib/clang/5.0.2/include/pmmintrin.h
flang/lib/clang/5.0.2/include/popcntintrin.h
flang/lib/clang/5.0.2/include/prfchwintrin.h
flang/lib/clang/5.0.2/include/rdseedintrin.h
flang/lib/clang/5.0.2/include/rtmintrin.h
flang/lib/clang/5.0.2/include/s390intrin.h
flang/lib/clang/5.0.2/include/shaintrin.h
flang/lib/clang/5.0.2/include/smmintrin.h
flang/lib/clang/5.0.2/include/stdalign.h
flang/lib/clang/5.0.2/include/stdarg.h
flang/lib/clang/5.0.2/include/stdatomic.h
flang/lib/clang/5.0.2/include/stdbool.h
flang/lib/clang/5.0.2/include/stddef.h
flang/lib/clang/5.0.2/include/stdint.h
flang/lib/clang/5.0.2/include/stdnoreturn.h
flang/lib/clang/5.0.2/include/tbmintrin.h
flang/lib/clang/5.0.2/include/tgmath.h
flang/lib/clang/5.0.2/include/tmmintrin.h
flang/lib/clang/5.0.2/include/unwind.h
flang/lib/clang/5.0.2/include/vadefs.h
flang/lib/clang/5.0.2/include/varargs.h
flang/lib/clang/5.0.2/include/vecintrin.h
flang/lib/clang/5.0.2/include/wmmintrin.h
flang/lib/clang/5.0.2/include/x86intrin.h
flang/lib/clang/5.0.2/include/xmmintrin.h
flang/lib/clang/5.0.2/include/xopintrin.h
flang/lib/clang/5.0.2/include/xsavecintrin.h
flang/lib/clang/5.0.2/include/xsaveintrin.h
flang/lib/clang/5.0.2/include/xsaveoptintrin.h
flang/lib/clang/5.0.2/include/xsavesintrin.h
flang/lib/clang/5.0.2/include/xtestintrin.h
flang/lib/cmake/clang/ClangConfig.cmake
flang/lib/cmake/clang/ClangTargets-%%CMAKE_BUILD_TYPE%%.cmake
flang/lib/cmake/clang/ClangTargets.cmake
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2 changes: 1 addition & 1 deletion devel/py-pymarc/Makefile
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Original file line number Diff line number Diff line change
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# $FreeBSD$

PORTNAME= pymarc
PORTVERSION= 3.1.9
PORTVERSION= 3.1.10
PORTEPOCH= 1
CATEGORIES= devel python
MASTER_SITES= CHEESESHOP
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