@@ -13,7 +13,6 @@ r_packages:

 apt_packages:

   - libnetcdf-dev

-  - libhdf5-dev

   - netcdf-bin

 # Set CXX1X for R-devel, as R-devel does not detect CXX1X support for gcc 4.6.3,

@@ -20,7 +20,7 @@ Depends: Rcpp (>= 0.10.1), methods, utils

 Imports: Biobase, BiocGenerics (>= 0.13.6), ProtGenerics (>= 1.9.1)

 Suggests: msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19), knitr, XML

 VignetteBuilder: knitr

-LinkingTo: Rcpp, zlibbioc

+LinkingTo: Rcpp, zlibbioc, Rhdf5lib

 RcppModules: Ramp, Pwiz, Ident

 SystemRequirements: C++11, GNU make, NetCDF

 URL: https://github.com/sneumann/mzR/

@@ -114,9 +114,11 @@ ARCH_OBJS=./boost/libs/filesystem/src/path_traits.o \

 ./boost_aux/boost/nowide/iostream.o

 ARCH_CPPFLAGS=-fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB

 ARCH_LIBS=-lws2_32 -lz

+RHDF5_LIBS=$(shell echo 'Rhdf5lib::pkgconfig("PKG_CXX_LIBS")'| "${R_HOME}/bin/R" --vanilla --slave)  

 else

 ARCH_OBJS=./boost/libs/thread/src/pthread/once.o \

 ./boost/libs/thread/src/pthread/thread.o

+RHDF5_LIBS=`echo 'Rhdf5lib::pkgconfig("PKG_CXX_LIBS")'| "${R_HOME}/bin/R" --vanilla --slave`

 endif

 NC_CFLAGS=`nc-config --cflags || /bin/true`

@@ -140,7 +142,7 @@ PWIZ_LDFLAGS=-lhdf5_cpp -lpthread

 ## Use the R_HOME indirection to support installations of multiple R version

 PKG_CPPFLAGS=$(PWIZ_CPPFLAGS) $(NC_CFLAGS)  $(ARCH_CPPFLAGS)

-PKG_LIBS=$(PWIZ_LDFLAGS) $(NC_LIBS)  $(ARCH_LIBS)

+PKG_LIBS=$(PWIZ_LDFLAGS) $(RHDF5_LIBS) $(NC_LIBS)  $(ARCH_LIBS)

 all: clean $(SHLIB)