diff options
Diffstat (limited to 'gnu/packages/patches')
| -rw-r--r-- | gnu/packages/patches/4store-unset-preprocessor-directive.patch | 16 | ||||
| -rw-r--r-- | gnu/packages/patches/clang-3.5-libc-search-path.patch (renamed from gnu/packages/patches/clang-libc-search-path.patch) | 0 | ||||
| -rw-r--r-- | gnu/packages/patches/clang-6.0-libc-search-path.patch | 67 | ||||
| -rw-r--r-- | gnu/packages/patches/delly-use-system-libraries.patch | 56 | ||||
| -rw-r--r-- | gnu/packages/patches/libgnomeui-utf8.patch | 6 | ||||
| -rw-r--r-- | gnu/packages/patches/racket-fix-xform-issue.patch | 63 |
6 files changed, 205 insertions, 3 deletions
diff --git a/gnu/packages/patches/4store-unset-preprocessor-directive.patch b/gnu/packages/patches/4store-unset-preprocessor-directive.patch new file mode 100644 index 0000000000..c4b1d6eda4 --- /dev/null +++ b/gnu/packages/patches/4store-unset-preprocessor-directive.patch @@ -0,0 +1,16 @@ +This patch removes the _XOPEN_SOURCE preprocessor directive as it does not seem to be needed. +Setting it removes the definition of strdup, which is used in filter-datatypes.c. + +Patch by Roel Janssen <roel@gnu.org> +*** a/src/frontend/filter-datatypes.c 1970-01-01 01:00:00.000000000 +0100 +--- b/src/frontend/filter-datatypes.c 2018-04-03 17:39:23.177905592 +0200 +*************** +*** 18,24 **** + * Copyright (C) 2006 Steve Harris for Garlik + */ + +- #define _XOPEN_SOURCE + #include <stdlib.h> + #include <string.h> + #include <math.h> +--- 18,23 ---- diff --git a/gnu/packages/patches/clang-libc-search-path.patch b/gnu/packages/patches/clang-3.5-libc-search-path.patch index 50e4480239..50e4480239 100644 --- a/gnu/packages/patches/clang-libc-search-path.patch +++ b/gnu/packages/patches/clang-3.5-libc-search-path.patch diff --git a/gnu/packages/patches/clang-6.0-libc-search-path.patch b/gnu/packages/patches/clang-6.0-libc-search-path.patch new file mode 100644 index 0000000000..a62e8063c2 --- /dev/null +++ b/gnu/packages/patches/clang-6.0-libc-search-path.patch @@ -0,0 +1,67 @@ +Clang attempts to guess file names based on the OS and distro (yes!), +but unfortunately, that doesn't work for us. + +This patch makes it easy to insert libc's $libdir so that Clang passes the +correct absolute file name of crt1.o etc. to 'ld'. It also disables all +the distro-specific stuff and removes the hard-coded FHS directory names +to make sure Clang also works on non-GuixSD systems. + +--- cfe-6.0.0.src/lib/Driver/ToolChains/Linux.cpp ++++ cfe-6.0.0.src/lib/Driver/ToolChains/Linux.cpp +@@ -207,7 +207,9 @@ + PPaths.push_back(Twine(GCCInstallation.getParentLibPath() + "/../" + + GCCInstallation.getTriple().str() + "/bin") + .str()); +- ++ // Comment out the distro-specific tweaks so that they don't bite when ++ // using Guix on a foreign distro. ++#if 0 + Distro Distro(D.getVFS()); + + if (Distro.IsAlpineLinux()) { +@@ -255,6 +257,7 @@ + + if (IsAndroid || Distro.IsOpenSUSE()) + ExtraOpts.push_back("--enable-new-dtags"); ++#endif + + // The selection of paths to try here is designed to match the patterns which + // the GCC driver itself uses, as this is part of the GCC-compatible driver. +@@ -329,14 +332,12 @@ + addPathIfExists(D, D.Dir + "/../" + OSLibDir, Paths); + } + +- addPathIfExists(D, SysRoot + "/lib/" + MultiarchTriple, Paths); +- addPathIfExists(D, SysRoot + "/lib/../" + OSLibDir, Paths); +- addPathIfExists(D, SysRoot + "/usr/lib/" + MultiarchTriple, Paths); +- addPathIfExists(D, SysRoot + "/usr/lib/../" + OSLibDir, Paths); +- + // Try walking via the GCC triple path in case of biarch or multiarch GCC + // installations with strange symlinks. + if (GCCInstallation.isValid()) { ++ // The following code would end up adding things like ++ // "/usr/lib/x86_64-unknown-linux-gnu/../../lib64" to the search path. ++#if 0 + addPathIfExists(D, + SysRoot + "/usr/lib/" + GCCInstallation.getTriple().str() + + "/../../" + OSLibDir, +@@ -349,6 +350,7 @@ + BiarchSibling.gccSuffix(), + Paths); + } ++#endif + + // See comments above on the multilib variant for details of why this is + // included even from outside the sysroot. +@@ -373,8 +375,9 @@ + if (StringRef(D.Dir).startswith(SysRoot)) + addPathIfExists(D, D.Dir + "/../lib", Paths); + +- addPathIfExists(D, SysRoot + "/lib", Paths); +- addPathIfExists(D, SysRoot + "/usr/lib", Paths); ++ // Add libc's lib/ directory to the search path, so that crt1.o, crti.o, ++ // and friends can be found. ++ addPathIfExists(D, "@GLIBC_LIBDIR@", Paths); + } + + bool Linux::HasNativeLLVMSupport() const { return true; } diff --git a/gnu/packages/patches/delly-use-system-libraries.patch b/gnu/packages/patches/delly-use-system-libraries.patch new file mode 100644 index 0000000000..3315c2a176 --- /dev/null +++ b/gnu/packages/patches/delly-use-system-libraries.patch @@ -0,0 +1,56 @@ +--- a/Makefile 2017-04-09 12:48:15.000000000 +0200 ++++ b/Makefile 2017-06-21 14:26:02.749282787 +0200 +@@ -9,8 +9,8 @@ + + # Flags + CXX=g++ +-CXXFLAGS += -isystem ${SEQTK_ROOT} -isystem ${BOOST_ROOT} -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing +-LDFLAGS += -L${SEQTK_ROOT} -L${BOOST_ROOT}/stage/lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time ++CXXFLAGS += -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing ++LDFLAGS += -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time + + # Additional flags for release/debug + ifeq (${PARALLEL}, 1) +@@ -23,7 +23,7 @@ + ifeq (${STATIC}, 1) + LDFLAGS += -static -static-libgcc -pthread -lhts -lz + else +- LDFLAGS += -lhts -lz -Wl,-rpath,${SEQTK_ROOT},-rpath,${BOOST_ROOT}/stage/lib ++ LDFLAGS += -lhts -lz + endif + ifeq (${DEBUG}, 1) + CXXFLAGS += -g -O0 -fno-inline -DDEBUG +@@ -41,29 +41,17 @@ + DELLYSOURCES = $(wildcard src/*.h) $(wildcard src/*.cpp) + + # Targets +-TARGETS = .htslib .bcftools .boost src/delly src/cov src/dpe ++TARGETS = src/delly src/cov src/dpe + + all: $(TARGETS) + +-.htslib: $(HTSLIBSOURCES) +- cd src/htslib && make && make lib-static && cd ../../ && touch .htslib +- +-.bcftools: $(HTSLIBSOURCES) +- cd src/bcftools && make && cd ../../ && touch .bcftools +- +-.boost: $(BOOSTSOURCES) +- cd src/modular-boost && ./bootstrap.sh --prefix=${PWD}/src/modular-boost --without-icu --with-libraries=iostreams,filesystem,system,program_options,date_time && ./b2 && ./b2 headers && cd ../../ && touch .boost +- +-src/delly: .htslib .bcftools .boost $(DELLYSOURCES) +- $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) +- +-src/cov: .htslib .bcftools .boost $(DELLYSOURCES) ++src/cov: $(DELLYSOURCES) + $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) + +-src/dpe: .htslib .bcftools .boost $(DELLYSOURCES) ++src/dpe: $(DELLYSOURCES) + $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) + + clean: + cd src/htslib && make clean + cd src/modular-boost && ./b2 --clean-all +- rm -f $(TARGETS) $(TARGETS:=.o) .htslib .boost .bcftools ++ rm -f $(TARGETS) $(TARGETS:=.o) diff --git a/gnu/packages/patches/libgnomeui-utf8.patch b/gnu/packages/patches/libgnomeui-utf8.patch index 304d74e1e2..11622b21ee 100644 --- a/gnu/packages/patches/libgnomeui-utf8.patch +++ b/gnu/packages/patches/libgnomeui-utf8.patch @@ -8,11 +8,11 @@ make[2]: Entering directory '/tmp/guix-build-libgnomeui-2.24.5.drv-0/libgnomeui- INFO: Reading ./gnome-marshal.list... GEN gnome-marshal.h Traceback (most recent call last): - File "/gnu/store/azh1is0xknn4xphwj33iqcb5ic9qhk8l-glib-2.54.2-bin/bin/glib-mkenums", line 688, in <module> + File "/gnu/store/...-glib-2.54.2-bin/bin/glib-mkenums", line 688, in <module> process_file(fname) - File "/gnu/store/azh1is0xknn4xphwj33iqcb5ic9qhk8l-glib-2.54.2-bin/bin/glib-mkenums", line 420, in process_file + File "/gnu/store/...-glib-2.54.2-bin/bin/glib-mkenums", line 420, in process_file line = curfile.readline() - File "/gnu/store/3lkypf5wnsnvkaidhw0pv7k3yjfh1r9g-python-3.6.3/lib/python3.6/codecs.py", line 321, in decode + File "/gnu/store/...-python-3.6.3/lib/python3.6/codecs.py", line 321, in decode (result, consumed) = self._buffer_decode(data, self.errors, final) UnicodeDecodeError: 'utf-8' codec can't decode byte 0xf1 in position 1009: invalid continuation byte make[2]: *** [Makefile:1109: stamp-gnometypebuiltins.h] Error 1 diff --git a/gnu/packages/patches/racket-fix-xform-issue.patch b/gnu/packages/patches/racket-fix-xform-issue.patch new file mode 100644 index 0000000000..0a1640ee51 --- /dev/null +++ b/gnu/packages/patches/racket-fix-xform-issue.patch @@ -0,0 +1,63 @@ +050cdb59839896b41431791f8ee0ef2564231b8f +Author: Matthew Flatt <mflatt@racket-lang.org> +AuthorDate: Tue Mar 6 09:05:08 2018 -0700 +Commit: Matthew Flatt <mflatt@racket-lang.org> +CommitDate: Tue Mar 6 09:05:08 2018 -0700 + +Parent: efb9a919fc ffi docs: clarification on `unsafe-socket->port` +Containing: master +Follows: v5.0.1 (21612) + +xform: avoid problems with `__signbitf128` + +Closes #1962 and uses the suggested patch there, among other changes. + +2 files changed, 6 insertions(+), 3 deletions(-) +racket/collects/compiler/private/xform.rkt | 2 +- +racket/src/racket/src/number.c | 7 +++++-- + +diff --git a/racket/collects/compiler/private/xform.rkt b/racket/collects/compiler/private/xform.rkt +index 28a425c057..89ae848f9c 100644 +--- a/collects/compiler/private/xform.rkt ++++ b/collects/compiler/private/xform.rkt +@@ -904,7 +904,7 @@ + + strlen cos cosl sin sinl exp expl pow powl log logl sqrt sqrtl atan2 atan2l frexp + isnan isinf fpclass signbit _signbit _fpclass __fpclassify __fpclassifyf __fpclassifyl +- _isnan __isfinited __isnanl __isnan __signbit __signbitf __signbitd __signbitl ++ _isnan __isfinited __isnanl __isnan __signbit __signbitf __signbitd __signbitl __signbitf128 + __isinff __isinfl isnanf isinff __isinfd __isnanf __isnand __isinf __isinff128 + __inline_isnanl __inline_isnan __inline_signbit __inline_signbitf __inline_signbitd __inline_signbitl + __builtin_popcount __builtin_clz __builtin_isnan __builtin_isinf __builtin_signbit +diff --git a/racket/src/racket/src/number.c b/racket/src/racket/src/number.c +index 71f42aaf3c..3bbad3ba83 100644 +--- a/src/racket/src/number.c ++++ b/src/racket/src/number.c +@@ -1796,6 +1796,7 @@ double scheme_real_to_double(Scheme_Object *r) + } + + XFORM_NONGCING static MZ_INLINE int minus_zero_p(double d) ++ XFORM_SKIP_PROC + { + #ifdef MZ_IS_NEG_ZERO + return MZ_IS_NEG_ZERO(d); +@@ -1809,7 +1810,9 @@ int scheme_minus_zero_p(double d) + return minus_zero_p(d); + } + +-static int rational_dbl_p(double f) { ++XFORM_NONGCING static int rational_dbl_p(double f) ++ XFORM_SKIP_PROC ++{ + return !(MZ_IS_NAN(f) + || MZ_IS_INFINITY(f)); + } +@@ -1955,7 +1958,7 @@ real_p(int argc, Scheme_Object *argv[]) + return (SCHEME_REALP(o) ? scheme_true : scheme_false); + } + +-static int is_rational(const Scheme_Object *o) ++XFORM_NONGCING static int is_rational(const Scheme_Object *o) + { + if (SCHEME_FLOATP(o)) + return rational_dbl_p(SCHEME_FLOAT_VAL(o));
\ No newline at end of file |