[Bioc-devel] mzR build failure on Windows: missing HDF5 libraries

[Neumann, Steffen]

Hi, 

compiling and linking is fixed now on all architectures,
thanks to the Rhdf5lib team for fixing/changing Rhdf5lib 
to allow unmodified code to link against it, and to Juhannes 
for testing. 

Have a nice day,
yours,
Steffen



On Mon, 2018-01-08 at 05:21 +0000, Rainer Johannes wrote:
> I'll test on mac and windows
> 
> cheers, jo
> 
> > On 7 Jan 2018, at 22:57, Neumann, Steffen <sneumann at ipb-halle.de>
> > wrote:
> > 
> > Hi,
> > 
> > Following the bug report in 
> > https://github.com/sneumann/mzR/issues/143
> > 
> > there is a branch with a fix in 
> > https://github.com/sneumann/mzR/pull/144
> > 
> > that passes Travis in 
> > https://travis-ci.org/sneumann/mzR/builds/324960762
> > 
> > which we can merge once there is a bit more testing
> > on other platforms. Any takers ?
> > 
> > Yours,
> > Steffen
> > 
> > 
> > 
> > On Fri, 2018-01-05 at 10:55 -0500, Martin Morgan wrote:
> > > Would be great, Steffen, to update mzR to use Rhdf5lib. I believe
> > > CRAN 
> > > packages with mzR dependencies are also failing to build under
> > > devel,
> > > as 
> > > well as xcms and other mzR dependencies in Bioc.
> > > 
> > > Martin
> > > 
> > > On 01/03/2018 04:18 AM, Mike Smith wrote:
> > > > Rhdf5lib is in the release branch too.  I'm happy to help try
> > > > and
> > > > get mzR
> > > > working with it.
> > > > 
> > > > On 2 January 2018 at 21:31, Martin Morgan <martin.morgan at roswel
> > > > lpar
> > > > k.org>
> > > > wrote:
> > > > 
> > > > > On 01/02/2018 03:16 PM, Neumann, Steffen wrote:
> > > > > 
> > > > > > Dear BioC team,
> > > > > > 
> > > > > > a happy new year to you as well ;-)
> > > > > > 
> > > > > > for a while we have a build error for mzR on windows
> > > > > > due to missing HDF5 libs:
> > > > > > https://github.com/sneumann/mzR/issues/143
> > > > > > 
> > > > > > I am looking for some hints how to fix this.
> > > > > > The https://bioconductor.org/packages/release/bioc/html/rhd
> > > > > > f5.h
> > > > > > tml
> > > > > > package has embedded rhdf5/src/libwin/x64/libhdf5ForBioC-
> > > > > > 7.dll
> > > > > > which we could try to use (It does not yet contain H5Cpp.h,
> > > > > > and we'd have to ask Bernd Fischer et al to include it.
> > > > > > 
> > > > > 
> > > > > Not a comprehensive answer or solution to release, but in
> > > > > devel
> > > > > there is
> > > > > Rhdf5lib which contains both the C and C++ headers. (I
> > > > > believe
> > > > > that rhdf5
> > > > > will move to using this library in the near future) Martin
> > > > > 
> > > > > 
> > > > > > ALternatively, it might already be present on the build
> > > > > > machines,
> > > > > > but we didn't have the include path set up:
> > > > > > https://github.com/r-hub/rhub/issues/91
> > > > > > "... the location of the hdf5 libraries is defined as
> > > > > > ${LIB_HDF5}/lib${R_ARCH}. "
> > > > > > 
> > > > > > So, any hints which way to go for a fix ?
> > > > > > 
> > > > > > Yours,
> > > > > > Steffen
> > > > > > 
> > > > > > 
> > > > > 
> > > > > This email message may contain legally privileged
> > > > > and/or...{{dropped:2}}
> > > > > 
> > > > > 
> > > > > _______________________________________________
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> > > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > > > > 
> > > > 
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> > > > 
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> > > > 
> > > 
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> > 
> > -- 
> > 
> > IPB Halle                    AG Massenspektrometrie & Bioinformatik
> > Dr. Steffen Neumann          http://www.IPB-Halle.DE
> > Weinberg 3                   http://msbi.bic-gh.de
> > 06120 Halle                  Tel. +49 (0) 345 5582 - 1470
> >                                  +49 (0) 345 5582 - 0
> > sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> 
-- 

IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
06120 Halle                  Tel. +49 (0) 345 5582 - 1470
                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409