Re: [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 +, Rainer Johannes wrote:
> I'll test on mac and windows
> 
> cheers, jo
> 
> > On 7 Jan 2018, at 22:57, Neumann, Steffen 
> > 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  > > > 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 HalleAG 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 HalleAG 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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Re: [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  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 >> 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
> 
> 
 
 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 HalleAG 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

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

[Neumann, Steffen]

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

[Martin Morgan]

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

[Mike Smith]

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 
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.html
>> 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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>

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

[Martin Morgan]

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

[Neumann, Steffen]

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.html
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.

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

-- 

IPB HalleAG 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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