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 <sneum...@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@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}} > > > > > > > > > > > > > > > _______________________________________________ > > > > > Bioc-devel@r-project.org mailing list > > > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > > > > > > > > > [[alternative HTML version deleted]] > > > > > > > > _______________________________________________ > > > > Bioc-devel@r-project.org mailing list > > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > > > > > > > > > This email message may contain legally privileged > > > and/or...{{dropped:2}} > > > > > > _______________________________________________ > > > Bioc-devel@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 > > _______________________________________________ > > Bioc-devel@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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
