Browse code

Fix compile errors by win_check()

uly55e5 authored on 24/01/2022 17:18:46
Showing1 changed files
... ...
@@ -38,6 +38,8 @@ PWIZOBJECTS=\
38 38
 ./boost/filesystem/src/codecvt_error_category.o \
39 39
 ./boost/thread/win32/thread.o \
40 40
 ./boost_aux/boost/nowide/iostream.o \
41
+./boost_aux/boost/nowide/filebuf.o \
42
+./boost_aux/libs/nowide/src/cstdio.o \
41 43
 ./pwiz/data/common/MemoryIndex.o \
42 44
 ./pwiz/data/common/CVTranslator.o \
43 45
 ./pwiz/data/common/cv.o \
... ...
@@ -105,6 +107,6 @@ all: libpwiz.a
105 107
 
106 108
 libpwiz.a: $(PWIZOBJECTS)
107 109
 	ar -rc $@ $(PWIZOBJECTS)
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-	
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+
109 111
 clean:
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-	rm -rf $(PWIZOBJECTS)
111 112
\ No newline at end of file
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+	rm -rf $(PWIZOBJECTS)
Browse code

Remove Ramp backend with dependencies

jorainer authored on 20/09/2021 12:19:56
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@@ -65,14 +65,12 @@ PWIZOBJECTS=\
65 65
 ./pwiz/data/msdata/IO.o \
66 66
 ./pwiz/data/msdata/SpectrumList_BTDX.o \
67 67
 ./pwiz/data/msdata/SpectrumInfo.o \
68
-./pwiz/data/msdata/RAMPAdapter.o \
69 68
 ./pwiz/data/msdata/LegacyAdapter.o \
70 69
 ./pwiz/data/msdata/SpectrumIterator.o \
71 70
 ./pwiz/data/msdata/MSDataFile.o \
72 71
 ./pwiz/data/msdata/MSNumpress.o \
73 72
 ./pwiz/data/msdata/SpectrumListCache.o \
74 73
 ./pwiz/data/msdata/Index_mzML.o \
75
-./pwiz/data/msdata/ramp/wglob.o \
76 74
 ./pwiz/data/identdata/IdentDataFile.o \
77 75
 ./pwiz/data/identdata/IdentData.o \
78 76
 ./pwiz/data/identdata/DefaultReaderList.o \
... ...
@@ -100,9 +98,7 @@ PWIZOBJECTS=\
100 98
 ./pwiz/utility/misc/SHA1.o \
101 99
 ./pwiz/utility/misc/SHA1Calculator.o \
102 100
 ./pwiz/utility/minimxml/XMLWriter.o \
103
-./pwiz/utility/minimxml/SAXParser.o \
104
-./random_access_gzFile.o \
105
-adler32.o compress.o crc32.o deflate.o gzclose.o gzlib.o gzread.o gzwrite.o infback.o inffast.o inflate.o inftrees.o trees.o uncompr.o zutil.o
101
+./pwiz/utility/minimxml/SAXParser.o
106 102
 
107 103
 
108 104
 all: libpwiz.a
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 0b3d4d9bb71e3ca5891b777610fc8dec103a6d61

Bumped version after KK's updates


Commit id: 9e04409b64757a177893d56c0300904f31945cb1

modified: src/pwiz/data/common/BinaryIndexStream.cpp modified: src/win/i386/libpwiz.a modified: src/win/x64/libpwiz.a


Commit id: f16b04258dc20bf3315beac99708e11728cfc12b

update precompiled lib for windows


Commit id: 5d56197f1148378d92e89b2d0a167e18c4b7ab2e

Bump version, tame .Rbuildignore


Commit id: 432da5bd294c9b87f7761e15bc814c3785c21abf

Merge remote-tracking branch 'origin/boost_159'


Commit id: 92be978bf72d90c2222a19ddf365f6d1acc9f20d

upadte Makevars


Commit id: ae75037a780cead56c4d20bedf822c94fb413677

upgrade to boost 1.5.9



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@110126 bc3139a8-67e5-0310-9ffc-ced21a209358

s.neumann authored on 01/11/2015 22:33:47
Showing1 changed files
... ...
@@ -1,7 +1,7 @@
1 1
 CC = gcc
2 2
 CXX = g++
3 3
 
4
-CXXFLAGS = -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DPRE_BUILD -s -O2 -m64
4
+CXXFLAGS = -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DPRE_BUILD -s -O2
5 5
 
6 6
 .c.o:
7 7
 	$(CC) $(CXXFLAGS) -c -o $@ $<
... ...
@@ -36,7 +36,7 @@ PWIZOBJECTS=\
36 36
 ./boost/filesystem/src/utf8_codecvt_facet.o \
37 37
 ./boost/filesystem/src/windows_file_codecvt.o \
38 38
 ./boost/filesystem/src/codecvt_error_category.o \
39
-./boost/thread/src/win32/thread.o \
39
+./boost/thread/win32/thread.o \
40 40
 ./boost_aux/boost/nowide/iostream.o \
41 41
 ./pwiz/data/common/MemoryIndex.o \
42 42
 ./pwiz/data/common/CVTranslator.o \
Browse code

Revert to gcc 4.6.3-based toolchain

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@100974 bc3139a8-67e5-0310-9ffc-ced21a209358

d.tenenbaum authored on 21/03/2015 22:39:38
Showing1 changed files
... ...
@@ -1,7 +1,7 @@
1 1
 CC = gcc
2 2
 CXX = g++
3 3
 
4
-CXXFLAGS = -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DPRE_BUILD -s -O2 
4
+CXXFLAGS = -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DPRE_BUILD -s -O2 -m64
5 5
 
6 6
 .c.o:
7 7
 	$(CC) $(CXXFLAGS) -c -o $@ $<
... ...
@@ -111,4 +111,4 @@ libpwiz.a: $(PWIZOBJECTS)
111 111
 	ar -rc $@ $(PWIZOBJECTS)
112 112
 	
113 113
 clean:
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-	rm -rf $(PWIZOBJECTS)
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+	rm -rf $(PWIZOBJECTS)
115 115
\ No newline at end of file
Browse code

Rebuild pwiz using gcc 4.9.2 included in Rtools33

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@100702 bc3139a8-67e5-0310-9ffc-ced21a209358

d.tenenbaum authored on 15/03/2015 23:28:33
Showing1 changed files
... ...
@@ -1,7 +1,7 @@
1 1
 CC = gcc
2 2
 CXX = g++
3 3
 
4
-CXXFLAGS = -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DPRE_BUILD -s -O2 -m64
4
+CXXFLAGS = -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DPRE_BUILD -s -O2 
5 5
 
6 6
 .c.o:
7 7
 	$(CC) $(CXXFLAGS) -c -o $@ $<
... ...
@@ -111,4 +111,4 @@ libpwiz.a: $(PWIZOBJECTS)
111 111
 	ar -rc $@ $(PWIZOBJECTS)
112 112
 	
113 113
 clean:
114
-	rm -rf $(PWIZOBJECTS)
115 114
\ No newline at end of file
115
+	rm -rf $(PWIZOBJECTS)
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 88249b6cc026da41c1b7e1fd56a31ebb09886b63

update news file


Commit id: 0fdf09a1222fb35fa3aad924f91f12af3ca362b7

bump version and remove superflous BiocGenerics in suggests


Commit id: 3b75ebcc265aa86eb5bf6858df8d8ab96347d387

cleanup


Commit id: dbe5aaaa0c694d1b3d13162c5036b6692f9b94bc

remove bioczlib modified: DESCRIPTION modified: NAMESPACE


Commit id: a201346057cdfb4acd71befb063591f98fd3d884

prebuild libpwiz new file: Makefile new file: Makefile.libpwiz modified: Makevars.win new file: adler32.c new file: compress.c new file: crc32.c new file: crc32.h new file: deflate.c new file: deflate.h new file: gzclose.c new file: gzguts.h new file: gzlib.c new file: gzread.c new file: gzwrite.c new file: infback.c new file: inffast.c new file: inffast.h new file: inffixed.h new file: inflate.c new file: inflate.h new file: inftrees.c new file: inftrees.h modified: pwiz/data/msdata/BinaryDataEncoder.cpp modified: pwiz/data/msdata/MSData.cpp modified: pwiz/data/msdata/MSNumpress.cpp modified: pwiz/utility/chemistry/Chemistry.cpp modified: pwiz/utility/chemistry/Chemistry.hpp new file: trees.c new file: trees.h new file: uncompr.c new file: zconf.h new file: zlib.h new file: zutil.c new file: zutil.h modified: ../DESCRIPTION modified: ../R/AllGenerics.R modified: ../R/methods-mzR.R



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@100029 bc3139a8-67e5-0310-9ffc-ced21a209358

s.neumann authored on 01/03/2015 23:33:03
Showing1 changed files
1 1
new file mode 100644
... ...
@@ -0,0 +1,114 @@
1
+CC = gcc
2
+CXX = g++
3
+
4
+CXXFLAGS = -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DPRE_BUILD -s -O2 -m64
5
+
6
+.c.o:
7
+	$(CC) $(CXXFLAGS) -c -o $@ $<
8
+
9
+.cpp.o:
10
+	$(CXX) $(CXXFLAGS) -c -o $@ $<
11
+
12
+PWIZOBJECTS=\
13
+./boost/system/src/error_code.o \
14
+./boost/regex/src/posix_api.o \
15
+./boost/regex/src/fileiter.o \
16
+./boost/regex/src/regex_raw_buffer.o \
17
+./boost/regex/src/cregex.o \
18
+./boost/regex/src/regex_debug.o \
19
+./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 \
31
+./boost/iostreams/src/zlib.o \
32
+./boost/iostreams/src/file_descriptor.o \
33
+./boost/filesystem/src/operations.o \
34
+./boost/filesystem/src/path.o \
35
+./boost/filesystem/src/path_traits.o \
36
+./boost/filesystem/src/utf8_codecvt_facet.o \
37
+./boost/filesystem/src/windows_file_codecvt.o \
38
+./boost/filesystem/src/codecvt_error_category.o \
39
+./boost/thread/src/win32/thread.o \
40
+./boost_aux/boost/nowide/iostream.o \
41
+./pwiz/data/common/MemoryIndex.o \
42
+./pwiz/data/common/CVTranslator.o \
43
+./pwiz/data/common/cv.o \
44
+./pwiz/data/common/ParamTypes.o \
45
+./pwiz/data/common/BinaryIndexStream.o \
46
+./pwiz/data/common/diff_std.o \
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+./pwiz/data/common/Unimod.o \
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+./pwiz/data/msdata/Version.o \
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+./pwiz/data/msdata/SpectrumList_MGF.o \
50
+./pwiz/data/msdata/DefaultReaderList.o \
51
+./pwiz/data/msdata/ChromatogramList_mzML.o \
52
+./pwiz/data/msdata/examples.o \
53
+./pwiz/data/msdata/Serializer_mzML.o \
54
+./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 \
57
+./pwiz/data/msdata/Serializer_mzXML.o \
58
+./pwiz/data/msdata/SpectrumList_mzML.o \
59
+./pwiz/data/msdata/SpectrumList_MSn.o \
60
+./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 \
65
+./pwiz/data/msdata/IO.o \
66
+./pwiz/data/msdata/SpectrumList_BTDX.o \
67
+./pwiz/data/msdata/SpectrumInfo.o \
68
+./pwiz/data/msdata/RAMPAdapter.o \
69
+./pwiz/data/msdata/LegacyAdapter.o \
70
+./pwiz/data/msdata/SpectrumIterator.o \
71
+./pwiz/data/msdata/MSDataFile.o \
72
+./pwiz/data/msdata/MSNumpress.o \
73
+./pwiz/data/msdata/SpectrumListCache.o \
74
+./pwiz/data/msdata/Index_mzML.o \
75
+./pwiz/data/msdata/ramp/wglob.o \
76
+./pwiz/data/identdata/IdentDataFile.o \
77
+./pwiz/data/identdata/IdentData.o \
78
+./pwiz/data/identdata/DefaultReaderList.o \
79
+./pwiz/data/identdata/Reader.o \
80
+./pwiz/data/identdata/Serializer_protXML.o \
81
+./pwiz/data/identdata/Serializer_pepXML.o \
82
+./pwiz/data/identdata/Serializer_mzid.o \
83
+./pwiz/data/identdata/IO.o \
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+./pwiz/data/identdata/Version.o \
85
+./pwiz/data/identdata/References.o \
86
+./pwiz/data/proteome/Modification.o \
87
+./pwiz/data/proteome/Digestion.o \
88
+./pwiz/data/proteome/Peptide.o \
89
+./pwiz/data/proteome/AminoAcid.o \
90
+./pwiz/utility/chemistry/Chemistry.o \
91
+./pwiz/utility/chemistry/ChemistryData.o \
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+./pwiz/utility/chemistry/MZTolerance.o \
93
+./pwiz/utility/misc/IntegerSet.o \
94
+./pwiz/utility/misc/Base64.o \
95
+./pwiz/utility/misc/IterationListener.o \
96
+./pwiz/utility/misc/MSIHandler.o \
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+./pwiz/utility/misc/Filesystem.o \
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+./pwiz/utility/misc/TabReader.o \
99
+./pwiz/utility/misc/random_access_compressed_ifstream.o \
100
+./pwiz/utility/misc/SHA1.o \
101
+./pwiz/utility/misc/SHA1Calculator.o \
102
+./pwiz/utility/minimxml/XMLWriter.o \
103
+./pwiz/utility/minimxml/SAXParser.o \
104
+./random_access_gzFile.o \
105
+adler32.o compress.o crc32.o deflate.o gzclose.o gzlib.o gzread.o gzwrite.o infback.o inffast.o inflate.o inftrees.o trees.o uncompr.o zutil.o
106
+
107
+
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+all: libpwiz.a
109
+
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+libpwiz.a: $(PWIZOBJECTS)
111
+	ar -rc $@ $(PWIZOBJECTS)
112
+	
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+clean:
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+	rm -rf $(PWIZOBJECTS)
0 115
\ No newline at end of file