Browse code

Merge branch 'master' into devel

* master:
bump version and update readme
compile pwiz when installing on Windows

From: Laurent <lg390@cam.ac.uk>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@121436 bc3139a8-67e5-0310-9ffc-ced21a209358

Laurent Gatto authored on 27/09/2016 08:54:49
Showing 5 changed files

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@@ -2,7 +2,7 @@ Package: mzR
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 Type: Package
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 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
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        (mass spectrometry data)
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-Version: 2.7.7
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+Version: 2.7.8
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 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou
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 Maintainer: Bernd Fischer <b.fischer@dkfz.de>,
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 	    Steffen Neumann <sneumann@ipb-halle.de>,
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@@ -1,3 +1,7 @@
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+CHANGES IN VERSION 2.7.8
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+------------------------
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+ o compile pwiz when installing on Windows <2016-09-26 Mon>
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+ 
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 CHANGES IN VERSION 2.7.7
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 ------------------------
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  o add netcdf static lib; potential incompatibility <2016-09-22 Thu>
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@@ -1,7 +1,103 @@
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+PWIZOBJECTS=\
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+./boost/system/src/error_code.o \
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+./boost/regex/src/posix_api.o \
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+./boost/regex/src/fileiter.o \
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+./boost/regex/src/regex_raw_buffer.o \
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+./boost/regex/src/cregex.o \
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+./boost/regex/src/regex_debug.o \
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+./boost/regex/src/instances.o \
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+./boost/regex/src/icu.o \
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+./boost/regex/src/usinstances.o \
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+./boost/regex/src/regex.o \
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+./boost/regex/src/wide_posix_api.o \
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+./boost/regex/src/regex_traits_defaults.o \
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+./boost/regex/src/winstances.o \
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+./boost/regex/src/wc_regex_traits.o \
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+./boost/regex/src/c_regex_traits.o \
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+./boost/regex/src/cpp_regex_traits.o \
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+./boost/regex/src/static_mutex.o \
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+./boost/regex/src/w32_regex_traits.o \
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+./boost/iostreams/src/zlib.o \
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+./boost/iostreams/src/file_descriptor.o \
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+./boost/thread/pthread/once.o \
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+./boost/thread/pthread/thread.o \
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+./boost/filesystem/src/operations.o \
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+./boost/filesystem/src/path.o \
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+./boost/filesystem/src/utf8_codecvt_facet.o \
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+./boost/chrono/src/chrono.o \
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+./boost/chrono/src/process_cpu_clocks.o \
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+./boost/chrono/src/thread_clock.o \
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+./pwiz/data/msdata/Version.o \
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+./pwiz/data/common/MemoryIndex.o \
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+./pwiz/data/common/CVTranslator.o \
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+./pwiz/data/common/cv.o \
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+./pwiz/data/common/ParamTypes.o \
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+./pwiz/data/common/BinaryIndexStream.o \
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+./pwiz/data/common/diff_std.o \
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+./pwiz/data/common/Unimod.o \
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+./pwiz/data/msdata/SpectrumList_MGF.o \
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+./pwiz/data/msdata/DefaultReaderList.o \
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+./pwiz/data/msdata/ChromatogramList_mzML.o \
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+./pwiz/data/msdata/examples.o \
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+./pwiz/data/msdata/Serializer_mzML.o \
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+./pwiz/data/msdata/Serializer_MSn.o \
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+./pwiz/data/msdata/Reader.o \
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+./pwiz/data/msdata/Serializer_MGF.o \
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+./pwiz/data/msdata/Serializer_mzXML.o \
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+./pwiz/data/msdata/SpectrumList_mzML.o \
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+./pwiz/data/msdata/SpectrumList_MSn.o \
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+./pwiz/data/msdata/BinaryDataEncoder.o \
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+./pwiz/data/msdata/Diff.o \
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+./pwiz/data/msdata/MSData.o \
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+./pwiz/data/msdata/References.o \
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+./pwiz/data/msdata/SpectrumList_mzXML.o \
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+./pwiz/data/msdata/IO.o \
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+./pwiz/data/msdata/SpectrumList_BTDX.o \
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+./pwiz/data/msdata/SpectrumInfo.o \
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+./pwiz/data/msdata/RAMPAdapter.o \
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+./pwiz/data/msdata/LegacyAdapter.o \
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+./pwiz/data/msdata/SpectrumIterator.o \
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+./pwiz/data/msdata/MSDataFile.o \
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+./pwiz/data/msdata/MSNumpress.o \
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+./pwiz/data/msdata/SpectrumListCache.o \
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+./pwiz/data/msdata/Index_mzML.o \
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+./pwiz/data/msdata/SpectrumWorkerThreads.o \
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+./pwiz/data/identdata/IdentDataFile.o \
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+./pwiz/data/identdata/IdentData.o \
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+./pwiz/data/identdata/DefaultReaderList.o \
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+./pwiz/data/identdata/Reader.o \
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+./pwiz/data/identdata/Serializer_protXML.o \
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+./pwiz/data/identdata/Serializer_pepXML.o \
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+./pwiz/data/identdata/Serializer_mzid.o \
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+./pwiz/data/identdata/IO.o \
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+./pwiz/data/identdata/References.o \
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+./pwiz/data/identdata/MascotReader.o \
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+./pwiz/data/proteome/Modification.o \
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+./pwiz/data/proteome/Digestion.o \
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+./pwiz/data/proteome/Peptide.o \
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+./pwiz/data/proteome/AminoAcid.o \
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+./pwiz/utility/minimxml/XMLWriter.o \
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+./pwiz/utility/minimxml/SAXParser.o \
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+./pwiz/utility/chemistry/Chemistry.o \
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+./pwiz/utility/chemistry/ChemistryData.o \
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+./pwiz/utility/chemistry/MZTolerance.o \
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+./pwiz/utility/misc/IntegerSet.o \
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+./pwiz/utility/misc/Base64.o \
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+./pwiz/utility/misc/IterationListener.o \
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+./pwiz/utility/misc/MSIHandler.o \
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+./pwiz/utility/misc/Filesystem.o \
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+./pwiz/utility/misc/TabReader.o \
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+./pwiz/utility/misc/random_access_compressed_ifstream.o \
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+./pwiz/utility/misc/SHA1.o \
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+./pwiz/utility/misc/SHA1Calculator.o \
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+./pwiz/utility/misc/sha1calc.o \
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+./random_access_gzFile.o \
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+./RcppExports.o
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+
1 97
 
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 MZROBJECTS=cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o RcppExports.o
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-OBJECTS= $(MZROBJECTS) R_init_mzR.o rampR.o
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+OBJECTS= $(MZROBJECTS) $(PWIZOBJECTS) rampR.o R_init_mzR.o
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 PWIZ_CPPFLAGS=-I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE
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... ...
@@ -20,7 +116,7 @@ else
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 	LD_ULDAR="-Wl,--dynamic-linker=$(ULDAR)/ld.exe"
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 endif
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-PKG_LIBS = $(LD_ULDAR) $(shell $(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()" ) $(PWIZ_LDFLAGS) -L./win/$(R_ARCH) -lws2_32 -lnetcdf -lpwiz
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+PKG_LIBS = $(LD_ULDAR) $(shell $(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()" ) $(PWIZ_LDFLAGS) -L./win/$(R_ARCH) -lws2_32 -lnetcdf
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 all: clean $(SHLIB)
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deleted file mode 100644
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Binary files a/src/win/i386/libpwiz.a and /dev/null differ
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deleted file mode 100644
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Binary files a/src/win/x64/libpwiz.a and /dev/null differ