gentoo resync : 25.12.2017

4 files changed, 142 insertions, 1 deletions

diff --git a/sci-biology/cufflinks/Manifest b/sci-biology/cufflinks/Manifest
index 26e76f6dde26..57016b548680 100644
--- a/sci-biology/cufflinks/Manifest
+++ b/sci-biology/cufflinks/Manifest
@@ -1,7 +1,9 @@
 AUX cufflinks-2.2.1-boost-1.65-tr1-removal.patch 344 BLAKE2B af0287f43bfd37da352fc330e3f6e06d4c6946851c6d8760302078157c8073591ccf7b508e2debf35747837216cc15e952fd7128bca500547cc180061dc2f780 SHA512 774558e93cf57ca9e9361df2271119474c8726573ff4467af4836db863d87ff0f38fe7048c9287227f18d3541891bb7b433b5fa33567616eeecda2bb5b057e9a
 AUX cufflinks-2.2.1-flags.patch 1132 BLAKE2B 675fb86a95425ed0def259b6f316e443eddb0c80a3a4f78e724f85ca3b14e58c29bb59bbc80a61ee7dcfaeb404383ffe0e58669dedc95224913c8d43939fd799 SHA512 58ea036d55d0b4835a56ea66afc2359bdb3e022f1fda3cab8402e4a2d7c6eab00fae96c739f89a25ca1e7528dad02f20c5c944a198c1eeca245e8995fbaa8f12
+AUX cufflinks-2.2.1-format-security.patch 618 BLAKE2B 1a316055af35849333c8ccbd46079a4ee1096becde474151932317bb66f81eff27b80d15306d9432f69a42fa9202a7712f9eff9921b915a92f4094ad2eadc79b SHA512 61a8cfe31988b028636f97db06d6855d9fce4ff3548da70d7e791fde85b38c09376be63714b67a0dc3e112f1d543735a51ebc437fc0b32eff98e9bf13138ff3c
 AUX cufflinks-2.2.1-gcc6.patch 344 BLAKE2B 7534c9060e93f074718726e2cbf7df259ba298b447915a4162916977340d33e35a4fddbf3e1b662334b56d42ffb8e0a096c337b465b5952abe27d1248fd6d0f2 SHA512 1e8fc2e717c464e39aecf2c434857e962a809fd2a9f84bfca2b7230d5150d464262b579f1a8c13970767e929562d04994d60002834c98c204e089d2d2a8381c0
+AUX cufflinks-2.2.1-gcc7.patch 4133 BLAKE2B ac2fbf2ebadfe0e90d7163dbd839b2173a3a3a9925b25e2eba8775793545ed8e17e8075c9e562300fa0fae6fd7c35893c8bc892c3e79bd6645b2e3cf51acbdbf SHA512 cbcc2be9e1266e24801dc91ed776aa314761ac682274c103c4f4ad9c37f8ad02b63233f2a16608dd620ca67e89a21028142bdc059cbe5fd2fffdbdb3e38f0af8
 AUX cufflinks-2.2.1-samtools-legacy.patch 1105 BLAKE2B ceeb2236456f30598e0d98ce1eaa4fae908286704fb6912a19ccc008b3d41476b853cacc3fc545450dde7d883593a545110a440c044118875041f56077c963b3 SHA512 80c6eaadcfe6919d61b63efc83d3d618e939c3a1cd5e4977f936c41656a96c7c2dd71a1309d6b0422b1bf248a366643a62f011b30b37b4001efae5da04acaadf
 DIST cufflinks-2.2.1.tar.gz 766280 BLAKE2B 200ca88d15cdfca550a12a39cf69d4c41850532c76840d2a86a21654b317e28c7f35d36ba26105490e75d55c5527dd64da1ef3c14f2d467a60379c234a8e9e60 SHA512 4da7f3a6090ea8cf469a85208c91073abdcd8b0e71c51b0f7052ce8001c368055b9d9cb7726d463196f5b3ab0b4a49bf5241d321ac3fe061225ecc47b4ca209b
-EBUILD cufflinks-2.2.1-r2.ebuild 1187 BLAKE2B 6d688f33f3404055c9b0a52a442a1a9f5c0d25a77a55fbdcfad4b521a98c0be66eaa238f341745ec14a9207753547e2c1b24dfaf46e45a46aa6c6b94927cec55 SHA512 8894ed39cc003b86660453968ad4ba7013153e16ec22f7818dce541bcdfd241693139ad45996b8b42edce5412de1413f4ad0966bf5b04c5e9a39476458d14a82
+EBUILD cufflinks-2.2.1-r2.ebuild 1260 BLAKE2B d6a462ebb0ab2851622b70796b6fc436784273004623792c40d95ebcaf0bd6116efe9fc4bfc25ea6fdc8fa1a4bd961564bf32c79e96ab055309df52109c0ca7e SHA512 e18f4e22800d944f71bb498fd6d6de827ef1d6dc3a37b4aabfa9d8c253ee4663cdd3ed6758845f755e3061765cdf9dac1d1f52f5d42da5ccd80449f6f667b9b9
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild b/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild
index 89f8484fad6a..745baffad99d 100644
--- a/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild
+++ b/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild
@@ -31,6 +31,8 @@ PATCHES=(
 	"${FILESDIR}"/${P}-flags.patch
 	"${FILESDIR}"/${P}-gcc6.patch
 	"${FILESDIR}"/${P}-boost-1.65-tr1-removal.patch
+	"${FILESDIR}"/${P}-gcc7.patch
+	"${FILESDIR}"/${P}-format-security.patch
 )
 
 src_prepare() {
diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-format-security.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-format-security.patch
new file mode 100644
index 000000000000..fa13f78d8b52
--- /dev/null
+++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-format-security.patch
@@ -0,0 +1,16 @@
+Author: Andreas Tille <tille@debian.org>
+Date: Wed, 22 May 2013 13:27:40 +0200
+Description: When building with --format-security (Debhelper 9 hardening)
+ this patch is needed to build successfully
+
+--- a/src/locfit/makecmd.c
++++ b/src/locfit/makecmd.c
+@@ -200,7 +200,7 @@ char *cmdline;
+   /* vs is used to store the command line string. */
+   sprintf(vn,"=clstr%d",clcount);
+   vs = createvar(vn,STSYSTEM,1+strlen(cmdline),VCHAR);
+-  sprintf((char *)vdptr(vs),cmdline);
++  sprintf((char *)vdptr(vs),"%s",cmdline);
+ 
+   /* va is used to store pointers to the command line fields. */
+   sprintf(vn,"=cline%d",clcount);
diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc7.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc7.patch
new file mode 100644
index 000000000000..48fe6e10ac96
--- /dev/null
+++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc7.patch
@@ -0,0 +1,121 @@
+Author: Alex Mestiashvili <mailatgoogl@gmail.com>
+Origin: https://lists.debian.org/debian-med/2017/09/msg00021.html
+Bug-Debian: https://bugs.debian.org/871234
+Description: Fix gcc-7 build issue, thanks to Jeff Epler <jepler@unpythonic.net>
+--- a/src/GHash.hh
++++ b/src/GHash.hh
+@@ -88,7 +88,7 @@
+                                 //nextkey is SET to the corresponding key
+   GHashEntry* NextEntry() { //returns a pointer to a GHashEntry
+   	 register int pos=fCurrentEntry;
+-  	 while (pos<fCapacity && hash[pos].hash<0) pos++;
++  	 while (pos<fCapacity && (hash[pos].hash)<0) pos++;
+   	 if (pos==fCapacity) {
+   	                 fCurrentEntry=fCapacity;
+   	                 return NULL;
+@@ -186,7 +186,7 @@
+         x=HASH2(h,n);
+         GASSERT(1<=x && x<n);
+         while(k[p].hash!=-1) p=(p+x)%n;
+-        GASSERT(k[p].hash<0);
++        GASSERT((k[p].hash)<0);
+         k[p]=hash[i];
+         }
+       }
+@@ -225,7 +225,7 @@
+   GTRACE(("GHash::insert: key=\"%s\"\n",ky));
+   //GMessage("GHash::insert: key=\"%s\"\n",ky);
+   GASSERT(0<=i && i<fCapacity);
+-  GASSERT(hash[i].hash<0);
++  GASSERT((hash[i].hash)<0);
+   hash[i].hash=h;
+   hash[i].mark=mrk;
+   hash[i].key=Gstrdup(ky);
+@@ -266,7 +266,7 @@
+   GTRACE(("GHash::insert: key=\"%s\"\n",ky));
+   //GMessage("GHash::insert: key=\"%s\"\n",ky);
+   GASSERT(0<=i && i<fCapacity);
+-  GASSERT(hash[i].hash<0);
++  GASSERT((hash[i].hash)<0);
+   hash[i].hash=h;
+   hash[i].mark=mrk;
+   hash[i].key=(char *)ky;
+@@ -310,7 +310,7 @@
+   if(i==-1) i=p;
+   GTRACE(("GHash::replace: %08x: inserting: \"%s\"\n",this,ky));
+   GASSERT(0<=i && i<fCapacity);
+-  GASSERT(hash[i].hash<0);
++  GASSERT((hash[i].hash)<0);
+   hash[i].hash=h;
+   hash[i].mark=mrk;
+   hash[i].key=Gstrdup(ky);
+@@ -412,7 +412,7 @@
+ 
+ template <class OBJ> char* GHash<OBJ>::NextKey() {
+  register int pos=fCurrentEntry;
+- while (pos<fCapacity && hash[pos].hash<0) pos++;
++ while (pos<fCapacity && (hash[pos].hash)<0) pos++;
+  if (pos==fCapacity) {
+                  fCurrentEntry=fCapacity;
+                  return NULL;
+@@ -425,7 +425,7 @@
+ 
+ template <class OBJ> OBJ* GHash<OBJ>::NextData() {
+  register int pos=fCurrentEntry;
+- while (pos<fCapacity && hash[pos].hash<0) pos++;
++ while (pos<fCapacity && (hash[pos].hash)<0) pos++;
+  if (pos==fCapacity) {
+                  fCurrentEntry=fCapacity;
+                  return NULL;
+@@ -439,7 +439,7 @@
+ 
+ template <class OBJ> OBJ* GHash<OBJ>::NextData(char* &nextkey) {
+  register int pos=fCurrentEntry;
+- while (pos<fCapacity && hash[pos].hash<0) pos++;
++ while (pos<fCapacity && (hash[pos].hash)<0) pos++;
+  if (pos==fCapacity) {
+                  fCurrentEntry=fCapacity;
+                  nextkey=NULL;
+@@ -457,16 +457,16 @@
+ // Get first non-empty entry
+ template <class OBJ> int GHash<OBJ>::First() const {
+   register int pos=0;
+-  while(pos<fCapacity){ if(0<=hash[pos].hash) break; pos++; }
+-  GASSERT(fCapacity<=pos || 0<=hash[pos].hash);
++  while(pos<fCapacity){ if(0<=(hash[pos].hash)) break; pos++; }
++  GASSERT(fCapacity<=pos || 0<=(hash[pos].hash));
+   return pos;
+   }
+ 
+ // Get last non-empty entry
+ template <class OBJ> int GHash<OBJ>::Last() const {
+   register int pos=fCapacity-1;
+-  while(0<=pos){ if(0<=hash[pos].hash) break; pos--; }
+-  GASSERT(pos<0 || 0<=hash[pos].hash);
++  while(0<=pos){ if(0<=(hash[pos].hash)) break; pos--; }
++  GASSERT(pos<0 || 0<=(hash[pos].hash));
+   return pos;
+   }
+ 
+@@ -474,8 +474,8 @@
+ // Find next valid entry
+ template <class OBJ> int GHash<OBJ>::Next(int pos) const {
+   GASSERT(0<=pos && pos<fCapacity);
+-  while(++pos <= fCapacity-1){ if(0<=hash[pos].hash) break; }
+-  GASSERT(fCapacity<=pos || 0<=hash[pos].hash);
++  while(++pos <= fCapacity-1){ if(0<=(hash[pos].hash)) break; }
++  GASSERT(fCapacity<=pos || 0<=(hash[pos].hash));
+   return pos;
+   }
+ 
+@@ -483,8 +483,8 @@
+ // Find previous valid entry
+ template <class OBJ> int GHash<OBJ>::Prev(int pos) const {
+   GASSERT(0<=pos && pos<fCapacity);
+-  while(--pos >= 0){ if(0<=hash[pos].hash) break; }
+-  GASSERT(pos<0 || 0<=hash[pos].hash);
++  while(--pos >= 0){ if(0<=(hash[pos].hash)) break; }
++  GASSERT(pos<0 || 0<=(hash[pos].hash));
+   return pos;
+   }
+