gentoo resync : 28.04.2019

3 files changed, 22 insertions, 3 deletions

diff --git a/sci-biology/consed/Manifest b/sci-biology/consed/Manifest
index 9694dbfdb96e..07e6a1839807 100644
--- a/sci-biology/consed/Manifest
+++ b/sci-biology/consed/Manifest
@@ -1,7 +1,7 @@
-AUX consed-29-fix-build-system.patch 5614 BLAKE2B 8b145d01e5fa6935715e7775d8e415b43184c4dd067bb3ad3eb72ef870b6f18d254f73a1e512dfb55376473df5cd3af70b4050daddf354cbe7a61773aaa9a13a SHA512 ea649079d5dbff21206bf8f56729fc559f374120dd3336499677eb65fde247739f41efdb29a3df60225ec38efc6802608aa2410bf4ab77f8d76bfd31fdc710fa
+AUX consed-29-fix-build-system.patch 5614 BLAKE2B 2ec980906ee2f9c7b0cede7b3eabad78cdc3e9c3d95c58275dc849ff36ee4ef9fa53dd3b321729ae60c9f2d2fc1ca4cd0ee2448175410acca7ffe6266d66ac44 SHA512 92df40d6465685aec77d73db1f0eb7a79d4c26fbbf7d9764c4e0a83208e4ef97b45db1a8175239bd174bd56aeed7a5aa0111c7b99764910f7d6c0ac63aba187d
 AUX consed-29-fix-c++14.patch 9261 BLAKE2B ff70814b39780dbbabc70eb7555359e8aee2ef72b40b7e149e2f63ccaeedfe7e0dc8822cb2b5c79d57c33e621a59e0e1cd273e49a0976daef0bdeb52f4f46569 SHA512 be5cd76d36cf437c1113d09e540d98d0eb92b7e2e732f4a5a308066b8046b5628048203e791a0fa316e44a4cc127d027418a7f038406df22c3f60552f5b87789
 AUX consed-29-fix-perl-shebang.patch 17375 BLAKE2B e34a358569d594f4ab60fc3745a6a84cab781cbad860421f5ac322154df9635e13b2e2349c92f4271b0ca161eda87285ba89bf0801992954fecaa11575c8baf9 SHA512 4caed1ab7229e2b3e367f03a8d650cafed2974232fcd6daa08e62c90512d49e09caceb34c5bb65c67a588bab314165d72d8c1687393549d4107425df78e3218d
-AUX consed-29-fix-qa.patch 11168 BLAKE2B 139b52d402f27c8121a43f933a181aabf150c0c8836f2facc7b42909db3808fab1ceede30956d6b3c2462ad31b43e054c0bbf8552e57e6e41479d25eb111738b SHA512 088d774159b421666bf75f6f9f17ee83d488625d482d8d404bde12671025b1f03322bee5c50e792fbbd822c223fa5ee697cf99c7efc9fcbebc119314d02df604
+AUX consed-29-fix-qa.patch 11639 BLAKE2B 3b80fd91b60c09e69cb9fa9b8deb88393fd89f02a3a650076db275567725aeb4636bfe1fcc35f44c72be33ed9494796fa6dab1b4da8b4b9444ecc73ea9b141fb SHA512 083b23d03ef9a473b41fae21ce433cdd5cdd0948819fa9dcc6dbed3022e93674aaa8769894b9be69b5bccf47dd6e67435bdf0549a719ecc4c5517f89010c3988
 DIST consed-29-linux.tar.gz 36172715 BLAKE2B 6706576b404c0bccb7ed28ab6fe2dec86fdac6f7651406d3f30e35caac3e49a66b4762edace2133d2dfb776bbeb730b74797c7323deb950f2648a46c4594fe98 SHA512 63a95d84cb58009045a9d898c8b1a94f98516bed9189f624a5930338cc8f51562504257f309d945fafcc07e0811ffeea122b640789f75fbd6c94535178dab4dd
 DIST consed-29-sources.tar.gz 3258845 BLAKE2B 508763ff2a240047cff0a43ba4b9b9a7f9302c0a023478c6b08f86bb77fb2c12a62a9b16165fe6257fe6c86af853dabe279bd9e05632c3e112e3fb7fad2c6bd3 SHA512 fd711a65a02ef1238cca12b90fe7fa9b67da6c37d43cd105f38c7b6475fbc073c1f4d7f99703dec9d3a0a7a2a9317cb14999a114bb6f52589cb9b6e34700eb93
 EBUILD consed-29.ebuild 2727 BLAKE2B 09c3d1619c7c751c1b084bcf1bc25bd87cfa23f4d83b0b6432b9229f7ecbd05c4a424522f6cc4117d571fa2ce34dbde805b4d0224a95db5af0f200e21688b1f3 SHA512 86160fe6b03dcfddc756c3f6a5c15bcbfe6a94b3002fe4deb39157adfc445a52ee557fa7732f07711a6859357c475bc31cfa535563cb91efee4511281fdef854
diff --git a/sci-biology/consed/files/consed-29-fix-build-system.patch b/sci-biology/consed/files/consed-29-fix-build-system.patch
index 27c9c552fe3f..30819f93ac80 100644
--- a/sci-biology/consed/files/consed-29-fix-build-system.patch
+++ b/sci-biology/consed/files/consed-29-fix-build-system.patch
@@ -45,7 +45,7 @@ Make build system semi-sane:
 -/usr/X11R6/lib/libICE.a /usr/X11R6/lib/libXext.a /usr/X11R6/lib/libXmu.a \
 -/usr/X11R6/lib/libXp.a /usr/lib/libm.a /me1/gordon/samtools/samtools-0.1.18/libbam.a /me1/gordon/samtools/samtools-0.1.18/bcftools/libbcf.a /me1/gordon/zlib/zlib-1.2.5/libz.a
 +
-+MOTIF_LIBS ?= -lXt -lXm
++MOTIF_LIBS ?= -lXm -lXt
 +ALL_LIBS = $(LIBS) $(MOTIF_LIBS) $(X11_LIBS) $(SAMTOOLS_LIBS)
  
  
diff --git a/sci-biology/consed/files/consed-29-fix-qa.patch b/sci-biology/consed/files/consed-29-fix-qa.patch
index 5bdf0264d25b..90e180da0174 100644
--- a/sci-biology/consed/files/consed-29-fix-qa.patch
+++ b/sci-biology/consed/files/consed-29-fix-qa.patch
@@ -127,6 +127,25 @@ Fix various QA violations, due to
     printf( "x = %d\n", pEvent->x );
     printf( "y = %d\n", pEvent->y );
     printf( "x_root = %d\n", pEvent->x_root );
+--- a/parseAceFile.cpp
++++ b/parseAceFile.cpp
+@@ -45,6 +45,7 @@
+ using namespace std;
+ #include    "basesegment.h"
+ #include    <stdio.h>
++#include    <stddef.h>
+ #include    <string.h>
+ #include    <sstream>
+ #include    "mbt_errors.h"
+@@ -292,7 +293,7 @@
+    char* szPossibleComp = szReadName + nLength - nCOMP;
+ 
+    if (memcmp( szPossibleComp, szCOMP, nCOMP ) == 0 ) {
+-      szPossibleComp = '\0';
++      szPossibleComp = NULL;
+       return( true );
+    }
+    else
 --- a/phaster2PhdBall.cpp
 +++ b/phaster2PhdBall.cpp
 @@ -547,7 +547,7 @@