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50 changes: 42 additions & 8 deletions
50
0_RootFS/LLVMBootstrap@13/bundled/patches/0010-add-musl-triples.patch
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,26 +1,60 @@ | ||
| --- a/clang/lib/Driver/ToolChains/Gnu.cpp | ||
| +++ b/clang/lib/Driver/ToolChains/Gnu.cpp | ||
| @@ -2077,6 +2077,7 @@ void Generic_GCC::GCCInstallationDetector::AddDefaultGCCPrefixes( | ||
| @@ -2077,7 +2077,8 @@ void Generic_GCC::GCCInstallationDetector::AddDefaultGCCPrefixes( | ||
| static const char *const AArch64LibDirs[] = {"/lib64", "/lib"}; | ||
| static const char *const AArch64Triples[] = { | ||
| "aarch64-none-linux-gnu", "aarch64-linux-gnu", "aarch64-redhat-linux", | ||
| + "aarch64-linux-musl", | ||
| "aarch64-suse-linux", "aarch64-linux-android"}; | ||
| - "aarch64-suse-linux", "aarch64-linux-android"}; | ||
| + "aarch64-suse-linux", "aarch64-linux-android", "aarch64-linux-musl", | ||
| + }; | ||
| static const char *const AArch64beLibDirs[] = {"/lib"}; | ||
| static const char *const AArch64beTriples[] = {"aarch64_be-none-linux-gnu", | ||
| @@ -2105,6 +2106,7 @@ void Generic_GCC::GCCInstallationDetector::AddDefaultGCCPrefixes( | ||
| "aarch64_be-linux-gnu"}; | ||
| @@ -2089,6 +2090,10 @@ void Generic_GCC::GCCInstallationDetector::AddDefaultGCCPrefixes( | ||
| "armv7hl-redhat-linux-gnueabi", | ||
| "armv6hl-suse-linux-gnueabi", | ||
| "armv7hl-suse-linux-gnueabi"}; | ||
| + static const char *const ARMHFMuslTriples[] = { | ||
| + "arm-linux-musleabihf", "armv7l-linux-musleabihf", | ||
| + "armv6l-linux-musleabihf", | ||
| + }; | ||
| static const char *const ARMebLibDirs[] = {"/lib"}; | ||
| static const char *const ARMebTriples[] = {"armeb-linux-gnueabi", | ||
| "armeb-linux-androideabi"}; | ||
| @@ -2105,7 +2110,9 @@ void Generic_GCC::GCCInstallationDetector::AddDefaultGCCPrefixes( | ||
| "x86_64-redhat-linux", "x86_64-suse-linux", | ||
| "x86_64-manbo-linux-gnu", "x86_64-linux-gnu", | ||
| "x86_64-slackware-linux", "x86_64-unknown-linux", | ||
| - "x86_64-amazon-linux", "x86_64-linux-android"}; | ||
| + "x86_64-amazon-linux", "x86_64-linux-android", | ||
| + "x86_64-linux-musl", | ||
| "x86_64-amazon-linux", "x86_64-linux-android"}; | ||
| + }; | ||
| static const char *const X32Triples[] = {"x86_64-linux-gnux32", | ||
| "x86_64-pc-linux-gnux32"}; | ||
| @@ -2115,6 +2117,7 @@ void Generic_GCC::GCCInstallationDetector::AddDefaultGCCPrefixes( | ||
| "i686-pc-linux-gnu", "i386-redhat-linux6E", | ||
| static const char *const X32LibDirs[] = {"/libx32", "/lib"}; | ||
| @@ -2116,6 +2123,7 @@ void Generic_GCC::GCCInstallationDetector::AddDefaultGCCPrefixes( | ||
| "i686-redhat-linux", "i386-redhat-linux", | ||
| "i586-suse-linux", "i686-montavista-linux", | ||
| + "i686-linux-musl", | ||
| "i686-linux-android", "i686-gnu", | ||
| + "i686-linux-musl", | ||
| }; | ||
|
|
||
| static const char *const M68kLibDirs[] = {"/lib"}; | ||
| @@ -2321,6 +2329,8 @@ void Generic_GCC::GCCInstallationDetector::AddDefaultGCCPrefixes( | ||
| LibDirs.append(begin(ARMLibDirs), end(ARMLibDirs)); | ||
| if (TargetTriple.getEnvironment() == llvm::Triple::GNUEABIHF) { | ||
| TripleAliases.append(begin(ARMHFTriples), end(ARMHFTriples)); | ||
| + } else if (TargetTriple.getEnvironment() == llvm::Triple::MuslEABIHF) { | ||
| + TripleAliases.append(begin(ARMHFMuslTriples), end(ARMHFMuslTriples)); | ||
| } else { | ||
| TripleAliases.append(begin(ARMTriples), end(ARMTriples)); | ||
| } | ||
| @@ -2330,6 +2340,8 @@ void Generic_GCC::GCCInstallationDetector::AddDefaultGCCPrefixes( | ||
| LibDirs.append(begin(ARMebLibDirs), end(ARMebLibDirs)); | ||
| if (TargetTriple.getEnvironment() == llvm::Triple::GNUEABIHF) { | ||
| TripleAliases.append(begin(ARMebHFTriples), end(ARMebHFTriples)); | ||
| + } else if (TargetTriple.getEnvironment() == llvm::Triple::MuslEABIHF) { | ||
| + TripleAliases.append(begin(ARMHFMuslTriples), end(ARMHFMuslTriples)); | ||
| } else { | ||
| TripleAliases.append(begin(ARMebTriples), end(ARMebTriples)); | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,3 @@ | ||
| bundled/patches/fix-format-strings.patch -text diff | ||
| bundled/patches/fix-ptr-to-int-on-windows-64bit.patch -text diff | ||
| bundled/patches/isfinite.patch -text diff |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,59 @@ | ||
| # Note that this script can accept some limited command-line arguments, run | ||
| # `julia build_tarballs.jl --help` to see a usage message. | ||
| using BinaryBuilder, Pkg | ||
|
|
||
| name = "R2R" | ||
| version = v"1.0.6" | ||
|
|
||
| # Collection of sources required to complete build | ||
| sources = [ | ||
| ArchiveSource("https://sourceforge.net/projects/weinberg-r2r/files/R2R-1.0.6.tgz", | ||
| "1ba8f51db92866ebe1aeb3c056f17489bceefe2f67c5c0bbdfbddc0eee17743d"), | ||
| DirectorySource("./bundled") | ||
| ] | ||
|
|
||
| # Bash recipe for building across all platforms | ||
| script = raw""" | ||
| cd $WORKSPACE/srcdir/R2R-*/ | ||
| atomic_patch -p1 ../patches/fix-ptr-to-int-on-windows-64bit.patch | ||
| atomic_patch -p1 ../patches/isfinite.patch | ||
| atomic_patch -p1 ../patches/fix-format-strings.patch | ||
| update_configure_scripts --reconf | ||
| export CXXFLAGS="-std=c++11" | ||
| ./configure \ | ||
| --prefix=${prefix} --build=${MACHTYPE} --host=${target} \ | ||
| --enable-nlopt | ||
| make -j${nproc} | ||
| make install | ||
| # install manual | ||
| # mkdir "${prefix}/doc" | ||
| # cp R2R-manual.pdf "${prefix}/doc" | ||
| # install demos | ||
| # cp -r demo/ "${prefix}" | ||
| install_license r2r-gpl-text.txt | ||
| """ | ||
|
|
||
| # These are the platforms we will build for by default, unless further | ||
| # platforms are passed in on the command line | ||
| platforms = supported_platforms() | ||
| platforms = expand_cxxstring_abis(platforms) | ||
|
|
||
| # The products that we will ensure are always built | ||
| products = [ | ||
| ExecutableProduct("r2r", :r2r), | ||
| ] | ||
|
|
||
| # Dependencies that must be installed before this package can be built | ||
| dependencies = [ | ||
| Dependency(PackageSpec(name="NLopt_jll", uuid="079eb43e-fd8e-5478-9966-2cf3e3edb778")), | ||
| ] | ||
|
|
||
| # Build the tarballs, and possibly a `build.jl` as well. | ||
| build_tarballs(ARGS, name, version, sources, script, platforms, products, dependencies; | ||
| julia_compat="1.6", preferred_gcc_version = v"7") |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,68 @@ | ||
| diff --git a/src/ParseOneStockholm.cpp b/src/ParseOneStockholm.cpp | ||
| index c2399e4..c4ab211 100755 | ||
| --- a/src/ParseOneStockholm.cpp | ||
| +++ b/src/ParseOneStockholm.cpp | ||
| @@ -259,15 +259,15 @@ void DumpInfoFile(const OtherDrawingStuff& otherDrawingStuff,const DrawingParams | ||
|
|
||
| fprintf(f,"drawingName\t%s\n",otherDrawingStuff.name.c_str()); | ||
|
|
||
| - fprintf(f,"posToAlignCol\t%u\n",otherDrawingStuff.currPosToOriginalPosMap.size()); | ||
| + fprintf(f,"posToAlignCol\t%lu\n",otherDrawingStuff.currPosToOriginalPosMap.size()); | ||
| for (size_t pos=0; pos<otherDrawingStuff.currPosToOriginalPosMap.size(); pos++) { | ||
| - fprintf(f,"%u\t%d\n",pos,otherDrawingStuff.currPosToOriginalPosMap[pos]); | ||
| + fprintf(f,"%zu\t%d\n",pos,otherDrawingStuff.currPosToOriginalPosMap[pos]); | ||
| } | ||
|
|
||
| - fprintf(f,"layout\t%u\n",posInfoVector.size()); | ||
| + fprintf(f,"layout\t%lu\n",posInfoVector.size()); | ||
| for (size_t i=0; i<posInfoVector.size(); i++) { | ||
| const PosInfo& p=posInfoVector[i]; | ||
| - fprintf(f,"%u\t%s\t%lg\t%lg\t%d\t%d",i,p.nuc.c_str(),p.pos.GetX(),p.pos.GetY(),p.flipLeftRight?1:0,p.partOfCircleThreePrime.isPartOfCircle?1:0); | ||
| + fprintf(f,"%zu\t%s\t%lg\t%lg\t%d\t%d",i,p.nuc.c_str(),p.pos.GetX(),p.pos.GetY(),p.flipLeftRight?1:0,p.partOfCircleThreePrime.isPartOfCircle?1:0); | ||
| if (p.partOfCircleThreePrime.isPartOfCircle) { | ||
| fprintf(f,"\t0\t%lg\t%lg\t%d", // the first hard-coded '0' is for p.dir, which is undefined for circular | ||
| p.partOfCircleThreePrime.center.GetX(),p.partOfCircleThreePrime.center.GetY(),(!p.partOfCircleThreePrime.circleDoesNotIntersectNextPoint)?1:0); | ||
| @@ -3064,7 +3064,7 @@ void OneStockholm_try (IndividualStructList& structList,const OtherDrawingStuff& | ||
| if (doOneSeq) { | ||
| for (size_t i=0; i<posInfoVector.size(); i++) { | ||
| posInfoVector[i].cleavageCode=oneSeqCleavage[i]; | ||
| - printf("posInfoVector[%d].cleavageCode=%c\n",i,oneSeqCleavage[i]); | ||
| + printf("posInfoVector[%zu].cleavageCode=%c\n",i,oneSeqCleavage[i]); | ||
| if ((i+1)%10==0 && drawingParams.defaultOneseqLabeling && !disableOneSeqNumbering) { | ||
| if (!posInfoVector[i].nucTickLabel.empty()) { | ||
| posInfoVector[i].nucTickLabel += " , "; | ||
| @@ -3095,7 +3095,7 @@ void OneStockholm_try (IndividualStructList& structList,const OtherDrawingStuff& | ||
|
|
||
| if (n>1) { | ||
| doublyPaired=true; | ||
| - printf("ERROR: position %d (raw %d) belongs to two pairs in different SS_cons lines (%s)\n", | ||
| + printf("ERROR: position %d (raw %zu) belongs to two pairs in different SS_cons lines (%s)\n", | ||
| FindTextColOfPos(otherDrawingStuff,(int)i),i,ssNames.c_str()); | ||
| } | ||
| } | ||
| diff --git a/src/PositionBackbone_MultiStemCircularSolver.cpp b/src/PositionBackbone_MultiStemCircularSolver.cpp | ||
| index ccfa0a4..776ed08 100755 | ||
| --- a/src/PositionBackbone_MultiStemCircularSolver.cpp | ||
| +++ b/src/PositionBackbone_MultiStemCircularSolver.cpp | ||
| @@ -300,7 +300,7 @@ void DumpNucPosAtEachIterMessageReceiver::PreEvaluateObjectiveFunc (const vector | ||
| } | ||
| for (size_t stem=0; stem<stemPosVector.size(); stem++) { | ||
| double frac=stemPosVector[stem].circleIntersectFraction.Eval(problemVars); | ||
| - fprintf(f,"frac-intersect\t%d\t%lg\n",stem,frac); | ||
| + fprintf(f,"frac-intersect\t%zu\t%lg\n",stem,frac); | ||
| } | ||
| iter++; | ||
| } | ||
| diff --git a/src/RnaDrawer.cpp b/src/RnaDrawer.cpp | ||
| index 13f0654..14dec43 100755 | ||
| --- a/src/RnaDrawer.cpp | ||
| +++ b/src/RnaDrawer.cpp | ||
| @@ -492,7 +492,7 @@ void RnaDrawer::CheckPathError (LineOrArcList& l,size_t i,int lineNum) | ||
| printf("WARNING: some points along the backbone could not be joined in aesthetically pleasing ways. This is probably the fault of this program, as it does not have all cases implemented. The problematic segments will be drawn as a simple straight line. Subsequent warning messages will say which positions are problematic. Note that it is possible to have a connector from position X to position X (again), if that position has a variable-length backbone, terminal loop or hairpin.\n"); | ||
| warnedAboutBadConnectors=true; | ||
| } | ||
| - printf("WARNING: in %s I had problems with joining the backbone from text alignment column %d (raw %d) to column %d (raw %d). code %d. See note above. (cpp line #%d)\n", | ||
| + printf("WARNING: in %s I had problems with joining the backbone from text alignment column %d (raw %zu) to column %d (raw %zu). code %d. See note above. (cpp line #%d)\n", | ||
| otherDrawingStuff.name.c_str(), | ||
| FindTextColOfPos(otherDrawingStuff,(int)i),i, | ||
| FindTextColOfPos(otherDrawingStuff,(int)(i+1)),i+1, |
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