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sneumann / mzR

This is the git repository matching the Bioconductor package mzR: parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data)
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Compilation failure on Linux, unknown symbol #177

Closed sneumann closed 6 years ago

sneumann commented 6 years ago

Hi, there is a build failure on the BioC build farm: http://bioconductor.org/checkResults/devel/bioc-LATEST/mzR/malbec1-install.html and also the Debian docker images (see https://github.com/Bioconductor/bioc_docker/issues/56)

where the reason is that we have multiple - and incompatible! - versions of libhdf5 in the link stage: 

/usr/local/lib/R/site-library/Rhdf5lib/lib/libhdf5_cpp.a 
/usr/local/lib/R/site-library/Rhdf5lib/lib/libhdf5.a 
/usr/local/lib/R/site-library/Rhdf5lib/lib/libsz.a 
-lz -L/opt/lib/hdf5-18/lib/ -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lnetcdf -lhdf5_hl 
-lhdf5 -lpthread -lsz

The first are defined by echo 'Rhdf5lib::pkgconfig("PKG_CXX_LIBS")'| "${R_HOME}/bin/R" --vanilla the second are defined in through nc-config --libs

sneumann commented 6 years ago

This will magically disappear once we have merged https://github.com/sneumann/mzR/tree/featureRemovelibnetCDF

lgatto commented 6 years ago

I have meged/pushed to Bioc.