diff options
Diffstat (limited to 'gnu/packages/patches')
-rw-r--r-- | gnu/packages/patches/doc++-include-directives.patch | 224 | ||||
-rw-r--r-- | gnu/packages/patches/doc++-segfault-fix.patch | 169 | ||||
-rw-r--r-- | gnu/packages/patches/hdf5-config-date.patch | 21 | ||||
-rw-r--r-- | gnu/packages/patches/hypre-doc-tables.patch | 25 | ||||
-rw-r--r-- | gnu/packages/patches/hypre-ldflags.patch | 9 | ||||
-rw-r--r-- | gnu/packages/patches/libarchive-CVE-2016-1541.patch | 67 | ||||
-rw-r--r-- | gnu/packages/patches/netcdf-config-date.patch | 47 |
7 files changed, 562 insertions, 0 deletions
diff --git a/gnu/packages/patches/doc++-include-directives.patch b/gnu/packages/patches/doc++-include-directives.patch new file mode 100644 index 0000000000..a59a907c3b --- /dev/null +++ b/gnu/packages/patches/doc++-include-directives.patch @@ -0,0 +1,224 @@ +Adapted from https://sourceforge.net/p/docpp/patches/1/ + +--- doc++-3.4.10/src/comment.ll 2000-06-24 18:50:23.000000000 +0200 ++++ doc++-3.4.10/src/comment.ll 2012-09-17 11:14:50.744922841 +0200 +@@ -24,7 +24,7 @@ + + #include <assert.h> + #include <ctype.h> +-#include <iostream.h> ++#include <iostream> + #include <stdarg.h> + #include <stdio.h> + +--- doc++-3.4.10/src/cpp.ll 2002-05-09 08:11:14.000000000 +0200 ++++ doc++-3.4.10/src/cpp.ll 2012-09-17 11:15:21.184333236 +0200 +@@ -26,7 +26,7 @@ + + #include <assert.h> + #include <ctype.h> +-#include <iostream.h> ++#include <iostream> + #include <stdarg.h> + #include <stdio.h> + +--- doc++-3.4.10/src/datahashtable.h 2000-08-27 21:44:34.000000000 +0200 ++++ doc++-3.4.10/src/datahashtable.h 2012-09-17 11:22:59.442589960 +0200 +@@ -26,11 +26,13 @@ + #define _DATAHASHTABLE_H + + #include <assert.h> +-#include <iostream.h> ++#include <iostream> + #include <stdlib.h> + + #include "McDArray.h" + ++using namespace std; ++ + /* This should be a private subclass of #DataHashTable#. However, since cfront + is not able to compile this constrution, we had move the class to global + scope. +--- doc++-3.4.10/src/doc2dbsgml.ll 2002-05-09 08:11:14.000000000 +0200 ++++ doc++-3.4.10/src/doc2dbsgml.ll 2012-09-17 11:20:49.077259414 +0200 +@@ -22,8 +22,8 @@ + + %{ + #include <assert.h> +-#include <fstream.h> +-#include <iostream.h> ++#include <fstream> ++#include <iostream> + #include <stdio.h> + #include <stdlib.h> + #include <string.h> +@@ -36,6 +36,8 @@ + #undef YY_INPUT + #define YY_INPUT(buf, result, max_size) result = yyread(buf, max_size); + ++using namespace std; ++ + static Entry* current; + static int inPos; + static int lastContext; +--- doc++-3.4.10/src/doc2dbxml.ll 2002-05-09 08:11:14.000000000 +0200 ++++ doc++-3.4.10/src/doc2dbxml.ll 2012-09-17 11:20:22.264831159 +0200 +@@ -25,8 +25,8 @@ + + %{ + #include <assert.h> +-#include <fstream.h> +-#include <iostream.h> ++#include <fstream> ++#include <iostream> + #include <stdio.h> + #include <stdlib.h> + #include <string.h> +@@ -39,6 +39,8 @@ + #undef YY_INPUT + #define YY_INPUT(buf, result, max_size) result = yyread(buf, max_size); + ++using namespace std; ++ + static Entry* current; + static int inPos; + static int lastContext; +--- doc++-3.4.10/src/doc2html.ll 2000-07-17 23:17:24.000000000 +0200 ++++ doc++-3.4.10/src/doc2html.ll 2012-09-17 11:22:40.354469631 +0200 +@@ -29,6 +29,8 @@ + #include "doc.h" + #include "nametable.h" + ++using namespace std; ++ + extern NameTable gifs; + + #define YY_DECL int yylex() +--- doc++-3.4.10/src/doc2tex.ll 2000-11-05 17:21:16.000000000 +0100 ++++ doc++-3.4.10/src/doc2tex.ll 2012-09-17 11:23:22.210701715 +0200 +@@ -23,8 +23,8 @@ + + %{ + #include <assert.h> +-#include <fstream.h> +-#include <iostream.h> ++#include <fstream> ++#include <iostream> + #include <stdio.h> + #include <stdlib.h> + #include <string.h> +@@ -38,6 +38,8 @@ + #undef YY_INPUT + #define YY_INPUT(buf, result, max_size) result = yyread(buf, max_size); + ++using namespace std; ++ + static Entry* current; + static int inPos; + static int lastContext; +--- doc++-3.4.10/src/doc.ll 2000-09-17 21:41:17.000000000 +0200 ++++ doc++-3.4.10/src/doc.ll 2012-09-17 11:15:37.068009454 +0200 +@@ -23,8 +23,8 @@ + + %{ + #include <assert.h> +-#include <fstream.h> +-#include <iostream.h> ++#include <fstream> ++#include <iostream> + #include <stdio.h> + #include <stdlib.h> + #include <string.h> +--- doc++-3.4.10/src/equate.cc 2002-05-02 21:13:10.000000000 +0200 ++++ doc++-3.4.10/src/equate.cc 2012-09-17 11:25:42.850669366 +0200 +@@ -23,9 +23,9 @@ + + #include "config.h" + +-#include <fstream.h> ++#include <fstream> + #include <getopt.h> +-#include <iostream.h> ++#include <iostream> + #include <stdio.h> + #include <string.h> + +--- doc++-3.4.10/src/html.cc 2001-02-17 07:34:49.000000000 +0100 ++++ doc++-3.4.10/src/html.cc 2012-09-17 11:24:07.978824681 +0200 +@@ -31,7 +31,7 @@ + #include <direct.h> + #endif + #include <errno.h> +-#include <iostream.h> ++#include <iostream> + #include <stdio.h> + #include <stdlib.h> + #include <string.h> +--- doc++-3.4.10/src/java.ll 2001-11-25 18:04:12.000000000 +0100 ++++ doc++-3.4.10/src/java.ll 2012-09-17 11:24:19.138834603 +0200 +@@ -26,7 +26,7 @@ + + #include <assert.h> + #include <ctype.h> +-#include <iostream.h> ++#include <iostream> + #include <stdio.h> + + #include "doc.h" +--- doc++-3.4.10/src/main.cc 2002-05-09 08:11:14.000000000 +0200 ++++ doc++-3.4.10/src/main.cc 2012-09-17 11:25:30.650719070 +0200 +@@ -25,7 +25,7 @@ + #include "config.h" + + #include <assert.h> +-#include <fstream.h> ++#include <fstream> + #include <getopt.h> + #include <locale.h> + #include <stdio.h> +--- doc++-3.4.10/src/nametable.cc 2000-04-08 23:11:54.000000000 +0200 ++++ doc++-3.4.10/src/nametable.cc 2012-09-17 11:25:58.894591128 +0200 +@@ -22,7 +22,7 @@ + */ + + #include <assert.h> +-#include <iostream.h> ++#include <iostream> + #include <stdlib.h> + #include <string.h> + +--- doc++-3.4.10/src/nametable.h 2000-04-08 23:11:56.000000000 +0200 ++++ doc++-3.4.10/src/nametable.h 2012-09-17 11:22:07.826207198 +0200 +@@ -25,7 +25,7 @@ + #define _NAME_TABLE_H + + #include <assert.h> +-#include <iostream.h> ++#include <iostream> + + #include "datahashtable.h" + +--- doc++-3.4.10/src/php.ll 2001-02-16 23:34:47.000000000 +0100 ++++ doc++-3.4.10/src/php.ll 2012-09-17 11:25:18.582759801 +0200 +@@ -23,7 +23,7 @@ + %{ + #include <assert.h> + #include <ctype.h> +-#include <iostream.h> ++#include <iostream> + #include <stdio.h> + + #include "doc.h" +--- doc++-3.4.10/src/tex2gif.cc 2001-08-07 20:55:40.000000000 +0200 ++++ doc++-3.4.10/src/tex2gif.cc 2012-09-17 11:26:06.698547836 +0200 +@@ -21,8 +21,8 @@ + Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. + */ + +-#include <iostream.h> +-#include <fstream.h> ++#include <iostream> ++#include <fstream> + #include <stdio.h> + #include <string.h> + diff --git a/gnu/packages/patches/doc++-segfault-fix.patch b/gnu/packages/patches/doc++-segfault-fix.patch new file mode 100644 index 0000000000..bad34c814e --- /dev/null +++ b/gnu/packages/patches/doc++-segfault-fix.patch @@ -0,0 +1,169 @@ +Adapted from https://sources.debian.net/data/main/d/doc%2B%2B/3.4.10-3.4/debian/patches/segfault_fix.patch + +--- doc++-3.4.10/src/McDArray.h 2000-07-30 12:40:48.000000000 +0200 ++++ doc++-3.4.10/src/McDArray.h 2005-05-10 15:02:06.000000000 +0200 +@@ -80,9 +80,14 @@ + McDArray(const McDArray& old) : memFactor(old.memFactor), + thesize(old.thesize), themax(old.themax) + { +- data = (T*)malloc(themax * sizeof(T)); +- if(thesize) +- memcpy(data, old.data, thesize * sizeof(T)); ++ if (themax) ++ { ++ data = (T*)malloc(themax * sizeof(T)); ++ if(thesize) ++ memcpy(data, old.data, thesize * sizeof(T)); ++ } ++ else ++ data = 0; + assert(isConsistent()); + } + +--- doc++-3.4.10/src/McDirectory.cc 2000-03-14 22:17:36.000000000 +0100 ++++ doc++-3.4.10/src/McDirectory.cc 2005-05-10 15:02:18.000000000 +0200 +@@ -23,12 +23,13 @@ + */ + + #include "McDirectory.h" +-#include "McSorter.h" + #include "McString.h" + #include "doc.h" + + #include <stdio.h> + ++#include <algorithm> ++ + #ifdef WIN32 + #include <windows.h> + #ifdef __BORLANDC__ +@@ -62,7 +63,7 @@ + FindClose(searchHandle); + StringCompare comp; + if(list.size()) +- sort((char **)list, list.size(), comp, 0); ++ std::sort((char **)list, (char **)list + list.size(), comp); + return 0; + } + +@@ -107,7 +108,7 @@ + closedir(dir); + StringCompare comp; + if(list.size()) +- sort((char **)list, list.size(), comp, 0); ++ std::sort((char **)list, (char **)list + list.size(), comp); + return list.size(); + } + +--- doc++-3.4.10/src/McDirectory.h 2000-06-28 21:54:58.000000000 +0200 ++++ doc++-3.4.10/src/McDirectory.h 2005-05-10 15:02:18.000000000 +0200 +@@ -59,9 +59,9 @@ + class StringCompare + { + public: +- int operator()(const char *t1, const char *t2) ++ bool operator()(const char *t1, const char *t2) + { +- return strcmp(t1, t2); ++ return strcmp(t1, t2) < 0; + } + }; + }; +--- doc++-3.4.10/src/html.cc 2001-02-17 07:34:49.000000000 +0100 ++++ doc++-3.4.10/src/html.cc 2005-05-10 15:02:18.000000000 +0200 +@@ -38,9 +38,10 @@ + #include <sys/stat.h> + #include <sys/types.h> + ++#include <algorithm> ++ + #include "McDirectory.h" + #include "McHashTable.h" +-#include "McSorter.h" + #include "classgraph.h" + #include "doc.h" + #include "gifs.h" +@@ -314,9 +315,11 @@ + virtual void writeMember(Entry *e, bool links, bool withSub = true); + class EntryCompare { + public: +- int operator()(const MemberWriterListEntry& l1, const MemberWriterListEntry& l2) ++ bool operator()(const MemberWriterListEntry& l1, const MemberWriterListEntry& l2) + { +- return strcmp(l1.entry->fullName.c_str(), l2.entry->fullName.c_str()); ++ const char *s1 = l1.entry->fullName.c_str(); ++ const char *s2 = l2.entry->fullName.c_str(); ++ return strcmp(s1, s2) < 0; + } + }; + public: +@@ -324,7 +327,7 @@ + { + EntryCompare comp; + if(list.size()) +- ::sort((MemberWriterListEntry *)list, list.size(), comp, 0); ++ std::sort((MemberWriterListEntry *)list, (MemberWriterListEntry *)list + list.size(), comp); + } + virtual void startList(FILE *f, char *heading, bool withLinks); + virtual void addMember(Entry *e, bool links, bool withSub = true) +@@ -376,7 +379,7 @@ + int lp; + + if(list.size() > 1) +- ::sort((TOCListEntry *)list, list.size(), comp, 0); ++ std::sort((TOCListEntry *)list, (TOCListEntry *)list + list.size(), comp); + + // Sort subsections + for(lp = 0; lp < list.size(); lp++) +@@ -385,9 +388,9 @@ + } + class EntryCompare { + public: +- int operator()(TOCListEntry& l1, TOCListEntry& l2) ++ bool operator()(const TOCListEntry& l1, const TOCListEntry& l2) + { +- return strcmp(l1.name, l2.name); ++ return strcmp(l1.name, l2.name) < 0; + } + }; + void addEntry(Entry *entry, TOClist *tl); +@@ -487,7 +490,7 @@ + + for(i = 0; i < list.size(); i++) + if(list[i].tl) +- free(list[i].tl); ++ delete list[i].tl; + } + + class HIERlist; +@@ -509,7 +512,7 @@ + int i; + + if(list.size() > 1) +- ::sort((HIERListEntry *)list, list.size(), comp, 0); ++ std::sort((HIERListEntry *)list, (HIERListEntry *)list + list.size(), comp); + + // Sort subentries + for(i = 0; i < list.size(); i++) +@@ -519,9 +522,9 @@ + class EntryCompare + { + public: +- int operator()(HIERListEntry& l1, HIERListEntry& l2) ++ bool operator()(const HIERListEntry& l1, const HIERListEntry& l2) + { +- return strcmp(l1.name, l2.name); ++ return strcmp(l1.name, l2.name) < 0; + } + }; + void addEntry(Entry *entry, HIERlist *hl); +--- doc++-3.4.10/src/readfiles.ll 2001-11-25 18:04:48.000000000 +0100 ++++ doc++-3.4.10/src/readfiles.ll 2005-05-10 15:02:18.000000000 +0200 +@@ -28,7 +28,6 @@ + #include <sys/types.h> + + #include "McDirectory.h" +-#include "McSorter.h" + #include "McString.h" + #include "doc.h" + #include "nametable.h" diff --git a/gnu/packages/patches/hdf5-config-date.patch b/gnu/packages/patches/hdf5-config-date.patch new file mode 100644 index 0000000000..c105435dc2 --- /dev/null +++ b/gnu/packages/patches/hdf5-config-date.patch @@ -0,0 +1,21 @@ +Honor SOURCE_DATE_EPOCH when exporting configuration date. +Autoconf-level patch submitted upstream on Wed Apr 13 17:03:23 UTC 2016 + +--- a/configure ++++ b/configure +@@ -27737,7 +28573,14 @@ + + + ## Configuration date +- CONFIG_DATE="`date`" ++ CONFIG_DATE="`date -u`" ++if test -n "$SOURCE_DATE_EPOCH"; then ++ CONFIG_DATE=`date -u -d "@$SOURCE_DATE_EPOCH" 2>/dev/null \ ++ || date -u -r "$SOURCE_DATE_EPOCH" 2>/dev/null` ++ if test -z "$CONFIG_DATE"; then ++ as_fn_error $? "malformed SOURCE_DATE_EPOCH" "$LINENO" 5 ++ fi ++fi + + ## User doing the configuration + CONFIG_USER="`whoami`@`hostname`" diff --git a/gnu/packages/patches/hypre-doc-tables.patch b/gnu/packages/patches/hypre-doc-tables.patch new file mode 100644 index 0000000000..6a852ee78e --- /dev/null +++ b/gnu/packages/patches/hypre-doc-tables.patch @@ -0,0 +1,25 @@ +Fixes doc++'s treatment of tabular within a parameter block. + +From commit 883925f8a at http://github.com/LLNL/hypre + +--- hypre-2.10.1/src/parcsr_ls/HYPRE_parcsr_ls.h 2015-12-04 22:12:19.000000000 -0600 ++++ hypre-2.10.1/src/parcsr_ls/HYPRE_parcsr_ls.h 2016-03-16 09:02:58.547501336 -0500 +@@ -1154,8 +1154,6 @@ + * Set the symmetry parameter for the + * ParaSails preconditioner. + * +- * @param solver [IN] Preconditioner object for which to set symmetry parameter. +- * @param sym [IN] Value of the symmetry parameter: + * \begin{tabular}{|c|l|} \hline + * value & meaning \\ \hline + * 0 & nonsymmetric and/or indefinite problem, and nonsymmetric preconditioner\\ +@@ -1163,6 +1161,9 @@ + * 2 & nonsymmetric, definite problem, and SPD (factored) preconditioner \\ + * \hline + * \end{tabular} ++ * ++ * @param solver [IN] Preconditioner object for which to set symmetry parameter. ++ * @param sym [IN] Value of the symmetry parameter: + **/ + HYPRE_Int HYPRE_ParaSailsSetSym(HYPRE_Solver solver, + HYPRE_Int sym); diff --git a/gnu/packages/patches/hypre-ldflags.patch b/gnu/packages/patches/hypre-ldflags.patch new file mode 100644 index 0000000000..a94fafa463 --- /dev/null +++ b/gnu/packages/patches/hypre-ldflags.patch @@ -0,0 +1,9 @@ +--- hypre-2.10.1/src/lib/Makefile.orig 2016-03-11 16:04:03.740259228 -0600 ++++ hypre-2.10.1/src/lib/Makefile 2016-03-11 16:04:57.296260190 -0600 +@@ -107,5 +107,5 @@ + + libHYPRE.so: ${FILES_HYPRE} + @echo "Building $@ ... " +- ${BUILD_CC_SHARED} -o ${SONAME} ${FILES_HYPRE} ${SOLIBS} ${SHARED_SET_SONAME}${SONAME} ${SHARED_OPTIONS} ++ ${BUILD_CC_SHARED} ${LDFLAGS} -o ${SONAME} ${FILES_HYPRE} ${SOLIBS} ${SHARED_SET_SONAME}${SONAME} ${SHARED_OPTIONS} + ln -s ${SONAME} $@ diff --git a/gnu/packages/patches/libarchive-CVE-2016-1541.patch b/gnu/packages/patches/libarchive-CVE-2016-1541.patch new file mode 100644 index 0000000000..6ac8773244 --- /dev/null +++ b/gnu/packages/patches/libarchive-CVE-2016-1541.patch @@ -0,0 +1,67 @@ +Fix CVE-2016-1541 (buffer overflow zip_read_mac_metadata) + +Taken from upstream source repository: +https://github.com/libarchive/libarchive/commit/d0331e8e5b05b475f20b1f3101fe1ad772d7e7e7 + +When reading OS X metadata entries in Zip archives that were stored +without compression, libarchive would use the uncompressed entry size +to allocate a buffer but would use the compressed entry size to limit +the amount of data copied into that buffer. Since the compressed +and uncompressed sizes are provided by data in the archive itself, +an attacker could manipulate these values to write data beyond +the end of the allocated buffer. + +This fix provides three new checks to guard against such +manipulation and to make libarchive generally more robust when +handling this type of entry: + 1. If an OS X metadata entry is stored without compression, + abort the entire archive if the compressed and uncompressed + data sizes do not match. + 2. When sanity-checking the size of an OS X metadata entry, + abort this entry if either the compressed or uncompressed + size is larger than 4MB. + 3. When copying data into the allocated buffer, check the copy + size against both the compressed entry size and uncompressed + entry size. +--- + libarchive/archive_read_support_format_zip.c | 13 +++++++++++++ + 1 file changed, 13 insertions(+) + +diff --git a/libarchive/archive_read_support_format_zip.c b/libarchive/archive_read_support_format_zip.c +index 0f8262c..0a0be96 100644 +--- a/libarchive/archive_read_support_format_zip.c ++++ b/libarchive/archive_read_support_format_zip.c +@@ -2778,6 +2778,11 @@ zip_read_mac_metadata(struct archive_read *a, struct archive_entry *entry, + + switch(rsrc->compression) { + case 0: /* No compression. */ ++ if (rsrc->uncompressed_size != rsrc->compressed_size) { ++ archive_set_error(&a->archive, ARCHIVE_ERRNO_FILE_FORMAT, ++ "Malformed OS X metadata entry: inconsistent size"); ++ return (ARCHIVE_FATAL); ++ } + #ifdef HAVE_ZLIB_H + case 8: /* Deflate compression. */ + #endif +@@ -2798,6 +2803,12 @@ zip_read_mac_metadata(struct archive_read *a, struct archive_entry *entry, + (intmax_t)rsrc->uncompressed_size); + return (ARCHIVE_WARN); + } ++ if (rsrc->compressed_size > (4 * 1024 * 1024)) { ++ archive_set_error(&a->archive, ARCHIVE_ERRNO_FILE_FORMAT, ++ "Mac metadata is too large: %jd > 4M bytes", ++ (intmax_t)rsrc->compressed_size); ++ return (ARCHIVE_WARN); ++ } + + metadata = malloc((size_t)rsrc->uncompressed_size); + if (metadata == NULL) { +@@ -2836,6 +2847,8 @@ zip_read_mac_metadata(struct archive_read *a, struct archive_entry *entry, + bytes_avail = remaining_bytes; + switch(rsrc->compression) { + case 0: /* No compression. */ ++ if ((size_t)bytes_avail > metadata_bytes) ++ bytes_avail = metadata_bytes; + memcpy(mp, p, bytes_avail); + bytes_used = (size_t)bytes_avail; + metadata_bytes -= bytes_used; diff --git a/gnu/packages/patches/netcdf-config-date.patch b/gnu/packages/patches/netcdf-config-date.patch new file mode 100644 index 0000000000..5054612e95 --- /dev/null +++ b/gnu/packages/patches/netcdf-config-date.patch @@ -0,0 +1,47 @@ +Honor SOURCE_DATE_EPOCH when exporting configuration date. +Autoconf-level patch submitted upstream on Fri Apr 15 23:07:42 UTC 2016 + +--- a/configure ++++ b/configure +@@ -2866,7 +2866,17 @@ + + + # Configuration Date +- CONFIG_DATE="`date`" ++ CONFIG_DATE="`date -u`" ++if test -n "$SOURCE_DATE_EPOCH"; then ++ CONFIG_DATE=`date -u -d "@$SOURCE_DATE_EPOCH" 2>/dev/null \ ++ || date -u -r "$SOURCE_DATE_EPOCH" 2>/dev/null` ++ if test -z "$CONFIG_DATE"; then ++ as_fn_error $? "malformed SOURCE_DATE_EPOCH" "$LINENO" 5 ++ fi ++fi ++cat >>confdefs.h <<_ACEOF ++#define CONFIG_DATE "$CONFIG_DATE" ++_ACEOF + + # Find out about the host we're building on. + ac_aux_dir= +--- a/libdispatch/derror.c ++++ b/libdispatch/derror.c +@@ -13,7 +13,7 @@ + #endif + + /* Tell the user the version of netCDF. */ +-static const char nc_libvers[] = PACKAGE_VERSION " of "__DATE__" "__TIME__" $"; ++static const char nc_libvers[] = PACKAGE_VERSION " of "CONFIG_DATE" $"; + + /** + \defgroup lib_version Library Version +--- a/config.h.in ++++ b/config.h.in +@@ -393,6 +393,9 @@ + /* Define to the version of this package. */ + #undef PACKAGE_VERSION + ++/* Define to the configuration date */ ++#undef CONFIG_DATE ++ + /* The size of `double', as computed by sizeof. */ + #undef SIZEOF_DOUBLE + |