From f6e11ca27fc77a5f958df61c33ea0cf50eb64331 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Jun 14 2014 08:03:36 +0000 Subject: More debuginfo path fixes --- diff --git a/BEDTools.spec b/BEDTools.spec index eb45e25..6b8c242 100644 --- a/BEDTools.spec +++ b/BEDTools.spec @@ -1,6 +1,6 @@ Name: BEDTools Version: 2.20.1 -Release: 1%{?dist} +Release: 2%{?dist} Summary: A flexible suite of utilities for comparing genomic features Group: Applications/Engineering @@ -11,6 +11,7 @@ Source0: https://github.com/arq5x/bedtools2/releases/download/v%{version}/bedtoo #Source1: http://bedtools.googlecode.com/files/%{name}-User-Manual.v4.pdf #Fix debuginfo canonicalization error Patch0: bedtools-gzstream-path.patch +Patch1: bedtools-debuginfo-path.patch BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n) BuildRequires: zlib-devel @@ -39,6 +40,7 @@ together. %prep %setup -q -n bedtools2-%{version} %patch0 -p1 -b .BEDTools.path +%patch1 -p1 -b .BEDTools.debuginfo # remove bundled curl library rm -rf src/utils/curl @@ -130,6 +132,9 @@ rm -rf %{buildroot} #%doc %{name}-User-Manual.v4.pdf %changelog +* Sat Jun 14 2014 Adam Huffman - 2.20.1-2 +- More path changes to fix debuginfo build + * Sat Jun 07 2014 Adam Huffman - 2.20.1-1 - Update to upstream 2.20.1 - Build integrated docs and remove obsolete PDF manual in -docs subpackage diff --git a/bedtools-debuginfo-path.patch b/bedtools-debuginfo-path.patch new file mode 100644 index 0000000..3eeb9b9 --- /dev/null +++ b/bedtools-debuginfo-path.patch @@ -0,0 +1,386 @@ +diff -ur bedtools2-2.20.1/src/utils/BamTools/Makefile bedtools2-2.20.1.new/src/utils/BamTools/Makefile +--- bedtools2-2.20.1/src/utils/BamTools/Makefile 2014-05-24 02:35:47.000000000 +0100 ++++ bedtools2-2.20.1.new/src/utils/BamTools/Makefile 2014-06-14 08:54:38.206849195 +0100 +@@ -1,7 +1,7 @@ + # ------------------- + # define our includes + # ------------------- +-OBJ_DIR = ../../../obj/ ++OBJ_DIR = ../../../obj + INCLUDES = -Isrc/ -Iinclude/ + + # ---------------------------------- +diff -ur bedtools2-2.20.1/src/utils/BamTools-Ancillary/Makefile bedtools2-2.20.1.new/src/utils/BamTools-Ancillary/Makefile +--- bedtools2-2.20.1/src/utils/BamTools-Ancillary/Makefile 2014-05-24 02:35:47.000000000 +0100 ++++ bedtools2-2.20.1.new/src/utils/BamTools-Ancillary/Makefile 2014-06-14 08:54:00.845394556 +0100 +@@ -1,6 +1,6 @@ +-OBJ_DIR = ../../../obj/ +-BIN_DIR = ../../../bin/ +-UTILITIES_DIR = ../ ++OBJ_DIR = ../../../obj ++BIN_DIR = ../../../bin ++UTILITIES_DIR = .. + + INCLUDES = -I$(UTILITIES_DIR)/BamTools/include \ + -I$(UTILITIES_DIR)/bedFile/ \ +@@ -27,4 +27,4 @@ + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +-.PHONY: clean +\ No newline at end of file ++.PHONY: clean +diff -ur bedtools2-2.20.1/src/utils/bedFile/Makefile bedtools2-2.20.1.new/src/utils/bedFile/Makefile +--- bedtools2-2.20.1/src/utils/bedFile/Makefile 2014-05-24 02:35:47.000000000 +0100 ++++ bedtools2-2.20.1.new/src/utils/bedFile/Makefile 2014-06-14 08:53:39.343406368 +0100 +@@ -1,6 +1,6 @@ +-OBJ_DIR = ../../../obj/ +-BIN_DIR = ../../../bin/ +-UTILITIES_DIR = ../../utils/ ++OBJ_DIR = ../../../obj ++BIN_DIR = ../../../bin ++UTILITIES_DIR = ../../utils + # ------------------- + # define our includes + # ------------------- +@@ -29,4 +29,4 @@ + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +-.PHONY: clean +\ No newline at end of file ++.PHONY: clean +diff -ur bedtools2-2.20.1/src/utils/bedFilePE/Makefile bedtools2-2.20.1.new/src/utils/bedFilePE/Makefile +--- bedtools2-2.20.1/src/utils/bedFilePE/Makefile 2014-05-24 02:35:47.000000000 +0100 ++++ bedtools2-2.20.1.new/src/utils/bedFilePE/Makefile 2014-06-14 08:53:13.494016197 +0100 +@@ -1,6 +1,6 @@ +-OBJ_DIR = ../../../obj/ +-BIN_DIR = ../../../bin/ +-UTILITIES_DIR = ../../utils/ ++OBJ_DIR = ../../../obj ++BIN_DIR = ../../../bin ++UTILITIES_DIR = ../../utils + # ------------------- + # define our includes + # ------------------- +@@ -26,4 +26,4 @@ + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +-.PHONY: clean +\ No newline at end of file ++.PHONY: clean +diff -ur bedtools2-2.20.1/src/utils/bedGraphFile/Makefile bedtools2-2.20.1.new/src/utils/bedGraphFile/Makefile +--- bedtools2-2.20.1/src/utils/bedGraphFile/Makefile 2014-05-24 02:35:47.000000000 +0100 ++++ bedtools2-2.20.1.new/src/utils/bedGraphFile/Makefile 2014-06-14 08:52:50.162858875 +0100 +@@ -1,6 +1,6 @@ +-OBJ_DIR = ../../../obj/ +-BIN_DIR = ../../../bin/ +-UTILITIES_DIR = ../../utils/ ++OBJ_DIR = ../../../obj ++BIN_DIR = ../../../bin ++UTILITIES_DIR = ../../utils + # ------------------- + # define our includes + # ------------------- +diff -ur bedtools2-2.20.1/src/utils/BinTree/Makefile bedtools2-2.20.1.new/src/utils/BinTree/Makefile +--- bedtools2-2.20.1/src/utils/BinTree/Makefile 2014-05-24 02:35:47.000000000 +0100 ++++ bedtools2-2.20.1.new/src/utils/BinTree/Makefile 2014-06-14 08:51:35.924994455 +0100 +@@ -1,6 +1,6 @@ +-OBJ_DIR = ../../../obj/ +-BIN_DIR = ../../../bin/ +-UTILITIES_DIR = ../../utils/ ++OBJ_DIR = ../../../obj ++BIN_DIR = ../../../bin ++UTILITIES_DIR = ../../utils + # ------------------- + # define our includes + # ------------------- +@@ -36,4 +36,4 @@ + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/BinTree.o + +-.PHONY: clean +\ No newline at end of file ++.PHONY: clean +diff -ur bedtools2-2.20.1/src/utils/BlockedIntervals/Makefile bedtools2-2.20.1.new/src/utils/BlockedIntervals/Makefile +--- bedtools2-2.20.1/src/utils/BlockedIntervals/Makefile 2014-05-24 02:35:47.000000000 +0100 ++++ bedtools2-2.20.1.new/src/utils/BlockedIntervals/Makefile 2014-06-14 08:50:30.322928549 +0100 +@@ -1,6 +1,6 @@ +-OBJ_DIR = ../../../obj/ +-BIN_DIR = ../../../bin/ +-UTILITIES_DIR = ../ ++OBJ_DIR = ../../../obj ++BIN_DIR = ../../../bin ++UTILITIES_DIR = .. + + INCLUDES = -I$(UTILITIES_DIR)/BamTools/include \ + -I$(UTILITIES_DIR)/bedFile/ \ +diff -ur bedtools2-2.20.1/src/utils/chromsweep/Makefile bedtools2-2.20.1.new/src/utils/chromsweep/Makefile +--- bedtools2-2.20.1/src/utils/chromsweep/Makefile 2014-05-24 02:35:47.000000000 +0100 ++++ bedtools2-2.20.1.new/src/utils/chromsweep/Makefile 2014-06-14 08:49:28.158180480 +0100 +@@ -1,6 +1,6 @@ +-OBJ_DIR = ../../../obj/ +-BIN_DIR = ../../../bin/ +-UTILITIES_DIR = ../../utils/ ++OBJ_DIR = ../../../obj ++BIN_DIR = ../../../bin ++UTILITIES_DIR = ../../utils + # ------------------- + # define our includes + # ------------------- +@@ -29,4 +29,4 @@ + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +-.PHONY: clean +\ No newline at end of file ++.PHONY: clean +diff -ur bedtools2-2.20.1/src/utils/Contexts/Makefile bedtools2-2.20.1.new/src/utils/Contexts/Makefile +--- bedtools2-2.20.1/src/utils/Contexts/Makefile 2014-05-24 02:35:47.000000000 +0100 ++++ bedtools2-2.20.1.new/src/utils/Contexts/Makefile 2014-06-14 08:50:03.671464219 +0100 +@@ -1,6 +1,6 @@ +-OBJ_DIR = ../../../obj/ +-BIN_DIR = ../../../bin/ +-UTILITIES_DIR = ../../utils/ ++OBJ_DIR = ../../../obj ++BIN_DIR = ../../../bin ++UTILITIES_DIR = ../../utils + # ------------------- + # define our includes + # ------------------- +@@ -43,4 +43,4 @@ + $(OBJ_DIR)/ContextMerge.o \ + $(OBJ_DIR)/ContextJaccard.o \ + +-.PHONY: clean +\ No newline at end of file ++.PHONY: clean +diff -ur bedtools2-2.20.1/src/utils/Fasta/Makefile bedtools2-2.20.1.new/src/utils/Fasta/Makefile +--- bedtools2-2.20.1/src/utils/Fasta/Makefile 2014-05-24 02:35:47.000000000 +0100 ++++ bedtools2-2.20.1.new/src/utils/Fasta/Makefile 2014-06-14 08:54:53.325247123 +0100 +@@ -1,6 +1,6 @@ +-OBJ_DIR = ../../../obj/ +-BIN_DIR = ../../../bin/ +-UTILITIES_DIR = ../../utils/ ++OBJ_DIR = ../../../obj ++BIN_DIR = ../../../bin ++UTILITIES_DIR = ../../utils + # ------------------- + # define our includes + # ------------------- +diff -ur bedtools2-2.20.1/src/utils/FileRecordTools/Makefile bedtools2-2.20.1.new/src/utils/FileRecordTools/Makefile +--- bedtools2-2.20.1/src/utils/FileRecordTools/Makefile 2014-05-24 02:35:47.000000000 +0100 ++++ bedtools2-2.20.1.new/src/utils/FileRecordTools/Makefile 2014-06-14 08:56:04.393818506 +0100 +@@ -1,6 +1,6 @@ +-OBJ_DIR = ../../../obj/ +-BIN_DIR = ../../../bin/ +-UTILITIES_DIR = ../../utils/ ++OBJ_DIR = ../../../obj ++BIN_DIR = ../../../bin ++UTILITIES_DIR = ../../utils + # ------------------- + # define our includes + # ------------------- +@@ -48,4 +48,4 @@ + @rm -f $(OBJ_DIR)/FileRecordMergeMgr.o + + +-.PHONY: clean +\ No newline at end of file ++.PHONY: clean +diff -ur bedtools2-2.20.1/src/utils/fileType/Makefile bedtools2-2.20.1.new/src/utils/fileType/Makefile +--- bedtools2-2.20.1/src/utils/fileType/Makefile 2014-05-24 02:35:47.000000000 +0100 ++++ bedtools2-2.20.1.new/src/utils/fileType/Makefile 2014-06-14 08:56:38.004926372 +0100 +@@ -1,6 +1,6 @@ +-OBJ_DIR = ../../../obj/ +-BIN_DIR = ../../../bin/ +-UTILITIES_DIR = ../../utils/ ++OBJ_DIR = ../../../obj ++BIN_DIR = ../../../bin ++UTILITIES_DIR = ../../utils + # ------------------- + # define our includes + # ------------------- +@@ -28,4 +28,4 @@ + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/fileType.o $(OBJ_DIR)/FileRecordTypeChecker.o + +-.PHONY: clean +\ No newline at end of file ++.PHONY: clean +diff -ur bedtools2-2.20.1/src/utils/general/Makefile bedtools2-2.20.1.new/src/utils/general/Makefile +--- bedtools2-2.20.1/src/utils/general/Makefile 2014-05-24 02:35:47.000000000 +0100 ++++ bedtools2-2.20.1.new/src/utils/general/Makefile 2014-06-14 08:56:59.510914933 +0100 +@@ -1,6 +1,6 @@ +-OBJ_DIR = ../../../obj/ +-BIN_DIR = ../../../bin/ +-UTILITIES_DIR = ../../utils/ ++OBJ_DIR = ../../../obj ++BIN_DIR = ../../../bin ++UTILITIES_DIR = ../../utils + # ------------------- + # define our includes + # ------------------- +diff -ur bedtools2-2.20.1/src/utils/GenomeFile/Makefile bedtools2-2.20.1.new/src/utils/GenomeFile/Makefile +--- bedtools2-2.20.1/src/utils/GenomeFile/Makefile 2014-05-24 02:35:47.000000000 +0100 ++++ bedtools2-2.20.1.new/src/utils/GenomeFile/Makefile 2014-06-14 08:57:15.329377595 +0100 +@@ -1,6 +1,6 @@ +-OBJ_DIR = ../../../obj/ +-BIN_DIR = ../../../bin/ +-UTILITIES_DIR = ../ ++OBJ_DIR = ../../../obj ++BIN_DIR = ../../../bin ++UTILITIES_DIR = .. + # ------------------- + # define our includes + # ------------------- +diff -ur bedtools2-2.20.1/src/utils/gzstream/Makefile bedtools2-2.20.1.new/src/utils/gzstream/Makefile +--- bedtools2-2.20.1/src/utils/gzstream/Makefile 2014-05-24 02:35:47.000000000 +0100 ++++ bedtools2-2.20.1.new/src/utils/gzstream/Makefile 2014-06-14 08:57:51.588730334 +0100 +@@ -33,9 +33,9 @@ + # ---------------------------------------------------------------------------- + + INCLUDES = -I. +-OBJ_DIR = ../../../obj/ +-BIN_DIR = ../../../bin/ +-UTILITIES_DIR = ../../utils/ ++OBJ_DIR = ../../../obj ++BIN_DIR = ../../../bin ++UTILITIES_DIR = ../../utils + + ${OBJ_DIR}/gzstream.o : gzstream.C gzstream.h + ${CXX} ${CXXFLAGS} -c -o ${OBJ_DIR}/gzstream.o gzstream.C $(INCLUDES) +diff -ur bedtools2-2.20.1/src/utils/KeyListOps/Makefile bedtools2-2.20.1.new/src/utils/KeyListOps/Makefile +--- bedtools2-2.20.1/src/utils/KeyListOps/Makefile 2014-05-24 02:35:47.000000000 +0100 ++++ bedtools2-2.20.1.new/src/utils/KeyListOps/Makefile 2014-06-14 08:58:07.554206590 +0100 +@@ -1,6 +1,6 @@ +-OBJ_DIR = ../../../obj/ +-BIN_DIR = ../../../bin/ +-UTILITIES_DIR = ../../utils/ ++OBJ_DIR = ../../../obj ++BIN_DIR = ../../../bin ++UTILITIES_DIR = ../../utils + # ------------------- + # define our includes + # ------------------- +@@ -40,4 +40,4 @@ + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/KeyListOps.o $(OBJ_DIR)/KeyListOpsMethods.o + +-.PHONY: clean +\ No newline at end of file ++.PHONY: clean +diff -ur bedtools2-2.20.1/src/utils/NewChromsweep/Makefile bedtools2-2.20.1.new/src/utils/NewChromsweep/Makefile +--- bedtools2-2.20.1/src/utils/NewChromsweep/Makefile 2014-05-24 02:35:47.000000000 +0100 ++++ bedtools2-2.20.1.new/src/utils/NewChromsweep/Makefile 2014-06-14 08:58:36.332867624 +0100 +@@ -1,6 +1,6 @@ +-OBJ_DIR = ../../../obj/ +-BIN_DIR = ../../../bin/ +-UTILITIES_DIR = ../../utils/ ++OBJ_DIR = ../../../obj ++BIN_DIR = ../../../bin ++UTILITIES_DIR = ../../utils + # ------------------- + # define our includes + # ------------------- +@@ -37,4 +37,4 @@ + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/NewChromsweep.o $(BIN_DIR)/NewChromsweep.o + +-.PHONY: clean +\ No newline at end of file ++.PHONY: clean +diff -ur bedtools2-2.20.1/src/utils/RecordOutputMgr/Makefile bedtools2-2.20.1.new/src/utils/RecordOutputMgr/Makefile +--- bedtools2-2.20.1/src/utils/RecordOutputMgr/Makefile 2014-05-24 02:35:47.000000000 +0100 ++++ bedtools2-2.20.1.new/src/utils/RecordOutputMgr/Makefile 2014-06-14 08:59:04.656486583 +0100 +@@ -1,6 +1,6 @@ +-OBJ_DIR = ../../../obj/ +-BIN_DIR = ../../../bin/ +-UTILITIES_DIR = ../../utils/ ++OBJ_DIR = ../../../obj ++BIN_DIR = ../../../bin ++UTILITIES_DIR = ../../utils + # ------------------- + # define our includes + # ------------------- +@@ -37,4 +37,4 @@ + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/RecordOutputMgr.o + +-.PHONY: clean +\ No newline at end of file ++.PHONY: clean +diff -ur bedtools2-2.20.1/src/utils/sequenceUtilities/Makefile bedtools2-2.20.1.new/src/utils/sequenceUtilities/Makefile +--- bedtools2-2.20.1/src/utils/sequenceUtilities/Makefile 2014-05-24 02:35:47.000000000 +0100 ++++ bedtools2-2.20.1.new/src/utils/sequenceUtilities/Makefile 2014-06-14 08:59:21.389033768 +0100 +@@ -1,6 +1,6 @@ +-OBJ_DIR = ../../../obj/ +-BIN_DIR = ../../../bin/ +-UTILITIES_DIR = ../../utils/ ++OBJ_DIR = ../../../obj ++BIN_DIR = ../../../bin ++UTILITIES_DIR = ../../utils + # ------------------- + # define our includes + # ------------------- +@@ -26,4 +26,4 @@ + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +-.PHONY: clean +\ No newline at end of file ++.PHONY: clean +diff -ur bedtools2-2.20.1/src/utils/tabFile/Makefile bedtools2-2.20.1.new/src/utils/tabFile/Makefile +--- bedtools2-2.20.1/src/utils/tabFile/Makefile 2014-05-24 02:35:47.000000000 +0100 ++++ bedtools2-2.20.1.new/src/utils/tabFile/Makefile 2014-06-14 08:59:43.699096681 +0100 +@@ -1,6 +1,6 @@ +-OBJ_DIR = ../../../obj/ +-BIN_DIR = ../../../bin/ +-UTILITIES_DIR = ../../utils/ ++OBJ_DIR = ../../../obj ++BIN_DIR = ../../../bin ++UTILITIES_DIR = ../../utils + # ------------------- + # define our includes + # ------------------- +@@ -28,4 +28,4 @@ + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +-.PHONY: clean +\ No newline at end of file ++.PHONY: clean +diff -ur bedtools2-2.20.1/src/utils/VectorOps/Makefile bedtools2-2.20.1.new/src/utils/VectorOps/Makefile +--- bedtools2-2.20.1/src/utils/VectorOps/Makefile 2014-05-24 02:35:47.000000000 +0100 ++++ bedtools2-2.20.1.new/src/utils/VectorOps/Makefile 2014-06-14 09:00:01.820772313 +0100 +@@ -1,6 +1,6 @@ +-OBJ_DIR = ../../../obj/ +-BIN_DIR = ../../../bin/ +-UTILITIES_DIR = ../../utils/ ++OBJ_DIR = ../../../obj ++BIN_DIR = ../../../bin ++UTILITIES_DIR = ../../utils + + # ---------------------------------- + # define our source and object files +@@ -17,4 +17,4 @@ + @echo "Cleaning up." + @rm -f $(OBJ_DIR)/* $(BIN_DIR)/* + +-.PHONY: clean +\ No newline at end of file ++.PHONY: clean +diff -ur bedtools2-2.20.1/src/utils/version/Makefile bedtools2-2.20.1.new/src/utils/version/Makefile +--- bedtools2-2.20.1/src/utils/version/Makefile 2014-05-24 02:35:47.000000000 +0100 ++++ bedtools2-2.20.1.new/src/utils/version/Makefile 2014-06-14 09:00:15.809065749 +0100 +@@ -1,6 +1,6 @@ +-OBJ_DIR = ../../../obj/ +-BIN_DIR = ../../../bin/ +-UTILITIES_DIR = ../../utils/ ++OBJ_DIR = ../../../obj ++BIN_DIR = ../../../bin ++UTILITIES_DIR = ../../utils + # ------------------- + # define our includes + # -------------------