commit: ccbd59a1a246014bf441e44a9f2bd8632a70c20e Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sun Dec 24 11:30:20 2017 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sun Dec 24 11:30:38 2017 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ccbd59a1
sci-biology/cufflinks: Fix building with GCC 7 Closes: https://bugs.gentoo.org/641580 Package-Manager: Portage-2.3.19, Repoman-2.3.6 sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild | 2 + .../files/cufflinks-2.2.1-format-security.patch | 16 +++ .../cufflinks/files/cufflinks-2.2.1-gcc7.patch | 121 +++++++++++++++++++++ 3 files changed, 139 insertions(+) diff --git a/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild b/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild index 89f8484fad6..745baffad99 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 00000000000..fa13f78d8b5 --- /dev/null +++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-format-security.patch @@ -0,0 +1,16 @@ +Author: Andreas Tille <[email protected]> +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 00000000000..48fe6e10ac9 --- /dev/null +++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc7.patch @@ -0,0 +1,121 @@ +Author: Alex Mestiashvili <[email protected]> +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 <[email protected]> +--- 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; + } +
