* 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
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@@ -2,7 +2,7 @@ Package: mzR |
| 2 | 2 |
Type: Package |
| 3 | 3 |
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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| 6 | 6 |
Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou |
| 7 | 7 |
Maintainer: Bernd Fischer <b.fischer@dkfz.de>, |
| 8 | 8 |
Steffen Neumann <sneumann@ipb-halle.de>, |
| ... | ... |
@@ -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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+ |
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| 1 | 97 |
|
| 2 | 98 |
MZROBJECTS=cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o RcppExports.o |
| 3 | 99 |
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-OBJECTS= $(MZROBJECTS) R_init_mzR.o rampR.o |
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+OBJECTS= $(MZROBJECTS) $(PWIZOBJECTS) rampR.o R_init_mzR.o |
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| 5 | 101 |
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| 6 | 102 |
PWIZ_CPPFLAGS=-I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE |
| 7 | 103 |
|
| ... | ... |
@@ -20,7 +116,7 @@ else |
| 20 | 116 |
LD_ULDAR="-Wl,--dynamic-linker=$(ULDAR)/ld.exe" |
| 21 | 117 |
endif |
| 22 | 118 |
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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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| 24 | 120 |
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| 25 | 121 |
all: clean $(SHLIB) |
| 26 | 122 |
|