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

[Rainer Johannes]

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 roswellpar
>>> 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/rhdf5.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
>>>>> 
>>>>> 
>>>> 
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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
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