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

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

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}}

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 roswellpark.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.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}}

	[[alternative HTML version deleted]]

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

This email message may contain legally privileged
and/or...{{dropped:2}}

	[[alternative HTML version deleted]]

This email message may contain legally privileged
and/or...{{dropped:2}}

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

This email message may contain legally privileged
and/or...{{dropped:2}}

	[[alternative HTML version deleted]]

This email message may contain legally privileged
and/or...{{dropped:2}}

-- 

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

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}}

	[[alternative HTML version deleted]]

This email message may contain legally privileged
and/or...{{dropped:2}}

-- 

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