mzR fails to build on bioc devel windows (hdf5 related)

[sgibb]

Since some time mzR fails to build from source on windows and bioc devel because of a missing hdf5 cpp header file (build report):

...
In file included from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27:0,
                 from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
pwiz/data/msdata/mz5/Datastructures_mz5.hpp:30:19: fatal error: H5Cpp.h: No such file or directory
 #include "H5Cpp.h"
                   ^
compilation terminated.
make: *** [pwiz/data/msdata/mz5/Configuration_mz5.o] Error 1
ERROR: compilation failed for package 'mzR'

The same error was present on Travis and my local machine which could be solved by adding libhdf5-dev as new dependency:

mzR/.travis.yml

Line 15 in 4c1f1d6

- libhdf5-dev

I guess this problem is related to the (re)introduction of mz5 (d4910ec; I don't want to start the discussion of #120 again; IMHO this code is merged so the PR could be closed anyway; the "automatic detection of HDF5" would be a different problem).

Is there a way to fix the build on bioc devel's windows machines? E.g. adding it to SystemRequirements in DESCRIPTION and/or inform the bioc build service maintainers that we need HDF5 cpp for windows?

[sneumann]

Hi,
following the suggestion by Martin Morgan on https://stat.ethz.ch/pipermail/bioc-devel/2018-January/012576.html I have started the branch https://github.com/sneumann/mzR/tree/feature/LinkToRhdf5lib
Note: since pwiz is including #include "H5Cpp.h"rather than #include "c++/H5Cpp.h" we need to find a fix for grimbough/Rhdf5lib#5
Locally I have worked around that by mv -i c++/H5* . inside /usr/local/lib/R/site-library/Rhdf5lib/include.
Yours, Steffen

[sneumann]

With some more workarounds on the travis side, I now have a successful build at https://travis-ci.org/sneumann/mzR/builds/324953759

[sneumann]

Fixed now in 2.13.3