For some reasons mz5 support was removed and re-added a few times during the
summer of 2014 - mz5 support was removed in May 26 18:28:05 2014,
added back in Jun 25 22:13:35 2014,
and removed again in July 11 01:48:50 2014. -
and resulted in its removal at the end of the summer at the merge
of the GSoC work [1]. No reason was mentioned.
The only reason I can think of, is that libhdf5_cpp is rare.
So this change add it back, and also fixes a somewhat stylistic issue
where PWIZ_LDFLAGS is defined but PKG_LIBS was not referring to it.
[1]
commit 84a4b1664f27a82bf12957dadc86443dd7c38705
Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: Sun Sep 28 18:06:01 2014 +0000
Commit made by the Bioconductor Git-SVN bridge.
Consists of 130 commits.
Commit information:
Commit id: 289dc240065888efcaa22ae75951e81f94fc800f
Fix package description after merge
Committed by: Steffen Neumann
Author Name: Steffen Neumann
Commit date: 2014-09-28 17:21:35 +0200
Author date: 2014-09-28 17:21:35 +0200
Commit id: 88248e8d6d86bb54dc260f0c55608dd1a949ade4
merged gsoc into master
...
Committed by: qkou
Author Name: qkou
Commit date: 2014-07-11 01:48:50 -0400
Author date: 2014-07-11 01:48:50 -0400
Commit id: 5f49d13b736cebd65484a5993cdcce253853d4e7
remove mz5
Closes https://github.com/sneumann/mzR/issues/118
Hin-Tak Leung authored on 13/08/2017 21:34:33
| ... | ... |
@@ -34,17 +34,26 @@ PWIZOBJECTS=\ |
| 34 | 34 |
./pwiz/data/common/BinaryIndexStream.o \ |
| 35 | 35 |
./pwiz/data/common/diff_std.o \ |
| 36 | 36 |
./pwiz/data/common/Unimod.o \ |
| 37 |
+./pwiz/data/msdata/mz5/Configuration_mz5.o \ |
|
| 38 |
+./pwiz/data/msdata/mz5/Connection_mz5.o \ |
|
| 39 |
+./pwiz/data/msdata/mz5/Datastructures_mz5.o \ |
|
| 40 |
+./pwiz/data/msdata/mz5/ReferenceRead_mz5.o \ |
|
| 41 |
+./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o \ |
|
| 42 |
+./pwiz/data/msdata/mz5/Translator_mz5.o \ |
|
| 37 | 43 |
./pwiz/data/msdata/SpectrumList_MGF.o \ |
| 38 | 44 |
./pwiz/data/msdata/DefaultReaderList.o \ |
| 39 | 45 |
./pwiz/data/msdata/ChromatogramList_mzML.o \ |
| 46 |
+./pwiz/data/msdata/ChromatogramList_mz5.o \ |
|
| 40 | 47 |
./pwiz/data/msdata/examples.o \ |
| 41 | 48 |
./pwiz/data/msdata/Serializer_mzML.o \ |
| 42 | 49 |
./pwiz/data/msdata/Serializer_MSn.o \ |
| 43 | 50 |
./pwiz/data/msdata/Reader.o \ |
| 51 |
+./pwiz/data/msdata/Serializer_mz5.o \ |
|
| 44 | 52 |
./pwiz/data/msdata/Serializer_MGF.o \ |
| 45 | 53 |
./pwiz/data/msdata/Serializer_mzXML.o \ |
| 46 | 54 |
./pwiz/data/msdata/SpectrumList_mzML.o \ |
| 47 | 55 |
./pwiz/data/msdata/SpectrumList_MSn.o \ |
| 56 |
+./pwiz/data/msdata/SpectrumList_mz5.o \ |
|
| 48 | 57 |
./pwiz/data/msdata/BinaryDataEncoder.o \ |
| 49 | 58 |
./pwiz/data/msdata/Diff.o \ |
| 50 | 59 |
./pwiz/data/msdata/MSData.o \ |
| ... | ... |
@@ -125,13 +134,13 @@ OBJECTS= $(MZROBJECTS) $(PWIZOBJECTS) $(ARCH_OBJS) rampR.o R_init_mzR.o |
| 125 | 134 |
## http://www.gamedev.net/topic/555511-is-there-a-way-to-only-disable-boost-debug-checks/ |
| 126 | 135 |
## |
| 127 | 136 |
|
| 128 |
-PWIZ_CPPFLAGS=-I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 |
|
| 129 |
-PWIZ_LDFLAGS=-lpthread |
|
| 137 |
+PWIZ_CPPFLAGS=-I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG |
|
| 138 |
+PWIZ_LDFLAGS=-lhdf5_cpp -lpthread |
|
| 130 | 139 |
|
| 131 | 140 |
## Use the R_HOME indirection to support installations of multiple R version |
| 132 | 141 |
PKG_CPPFLAGS=$(PWIZ_CPPFLAGS) $(NC_CFLAGS) $(ARCH_CPPFLAGS) |
| 133 | 142 |
|
| 134 |
-PKG_LIBS=$(NC_LIBS) $(ARCH_LIBS) |
|
| 143 |
+PKG_LIBS=$(PWIZ_LDFLAGS) $(NC_LIBS) $(ARCH_LIBS) |
|
| 135 | 144 |
|
| 136 | 145 |
all: clean $(SHLIB) |
| 137 | 146 |
|