725336ee48
This PR adds an updated version to the r-rhtslib package as well as fix the build. - add patches to use compiler flags from R - add variables for bzip2 and xz dependencies - use the spack Makeconf file when building the in-tree htslib - make patchelf available to allow R to remove reference to temporary installation directory in htslib shared object - Add new version of r-rsamtools as the r-rsamtools and r-rhtlib packages are closely paired.
19 lines
756 B
Diff
19 lines
756 B
Diff
--- a/src/htslib-1.7/Makefile.Rhtslib 2020-02-08 13:25:34.000000000 -0600
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+++ b/src/htslib-1.7/Makefile.Rhtslib 2020-02-08 21:02:01.434363322 -0600
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@@ -37,13 +37,13 @@
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# Default libraries to link if configure is not used
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htslib_default_libs = -lz -lm -lbz2 -llzma
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-CPPFLAGS += -D_FILE_OFFSET_BITS=64
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+CPPFLAGS += -D_FILE_OFFSET_BITS=64 $(BZIP2_INCLUDE) $(XZ_INCLUDE)
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# TODO: probably update cram code to make it compile cleanly with -Wc++-compat
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# For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
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#CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__
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CFLAGS += -fpic
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EXTRA_CFLAGS_PIC =
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-#LDFLAGS =
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+LDFLAGS += $(BZIP2_LIB) $(XZ_LIB)
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LIBS = $(htslib_default_libs)
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prefix = /usr/local
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