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[5.8-stable] math/hdf5

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[5.8-stable] math/hdf5

Adam Jensen
===> octave-4.0.0 depends on: hdf5-* - not found
===>  Verifying install for hdf5-* in math/hdf5
===>  Checking files for hdf5-1.8.15pl1p0
>> Fetch http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.15-patch1.tar.gz
ftp: Error retrieving file: 404 Not Found
>> Fetch http://ftp.openbsd.org/pub/OpenBSD/distfiles//hdf5-1.8.15-patch1.tar.gz
ftp: Error retrieving file: 404 Not Found
>> Fetch ftp://ftp.usa.openbsd.org/pub/OpenBSD/distfiles//hdf5-1.8.15-patch1.tar.gz
hdf5-1.8.15-patch1.tar.gz: No such file or directory.
>> Fetch http://ftp.fr.openbsd.org/pub/OpenBSD/distfiles//hdf5-1.8.15-patch1.tar.gz
ftp: Error retrieving file: 404 Not Found
*** Error 1 in /usr/ports/math/hdf5 (/usr/ports/infrastructure/mk/bsd.port.mk:2954 '/usr/ports/distfiles/hdf5-1.8.15-patch1.tar.gz': @lock=h...)
*** Error 1 in /usr/ports/math/hdf5 (/usr/ports/infrastructure/mk/bsd.port.mk:2321 '_internal-fetch')
*** Error 1 in /usr/ports/math/hdf5 (/usr/ports/infrastructure/mk/bsd.port.mk:2575 '/usr/ports/pobj/hdf5-1.8.15pl1/.extract_done')
*** Error 1 in /usr/ports/math/hdf5 (/usr/ports/infrastructure/mk/bsd.port.mk:1952 '/usr/ports/packages/i386/all/hdf5-1.8.15pl1p0.tgz')
*** Error 1 in /usr/ports/math/hdf5 (/usr/ports/infrastructure/mk/bsd.port.mk:2508 '_internal-package')
*** Error 1 in /usr/ports/math/hdf5 (/usr/ports/infrastructure/mk/bsd.port.mk:2488 'package')
*** Error 1 in /usr/ports/math/hdf5 (/usr/ports/infrastructure/mk/bsd.port.mk:1969 '/var/db/pkg/hdf5-1.8.15pl1p0/+CONTENTS')
*** Error 1 in /usr/ports/math/hdf5 (/usr/ports/infrastructure/mk/bsd.port.mk:2488 'install')
*** Error 1 in . (/usr/ports/infrastructure/mk/bsd.port.mk:2112 '/usr/ports/pobj/octave-4.0.0/.dep-math-hdf5')
*** Error 1 in . (/usr/ports/infrastructure/mk/bsd.port.mk:2575 '/usr/ports/pobj/octave-4.0.0/.extract_done')
*** Error 1 in . (/usr/ports/infrastructure/mk/bsd.port.mk:1952 '/usr/ports/packages/i386/all/octave-4.0.0.tgz')
*** Error 1 in . (/usr/ports/infrastructure/mk/bsd.port.mk:2508 '_internal-package')
*** Error 1 in . (/usr/ports/infrastructure/mk/bsd.port.mk:2488 'package')
*** Error 1 in . (/usr/ports/infrastructure/mk/bsd.port.mk:1969 '/var/db/pkg/octave-4.0.0/+CONTENTS')
*** Error 1 in /usr/ports/math/octave (/usr/ports/infrastructure/mk/bsd.port.mk:2488 'install')

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Re: [5.8-stable] math/hdf5

Juan Francisco Cantero Hurtado
On Wed, Feb 17, 2016 at 02:58:43PM -0500, Adam Jensen wrote:

> ===> octave-4.0.0 depends on: hdf5-* - not found
> ===>  Verifying install for hdf5-* in math/hdf5
> ===>  Checking files for hdf5-1.8.15pl1p0
> >> Fetch http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.15-patch1.tar.gz
> ftp: Error retrieving file: 404 Not Found
> >> Fetch http://ftp.openbsd.org/pub/OpenBSD/distfiles//hdf5-1.8.15-patch1.tar.gz
> ftp: Error retrieving file: 404 Not Found
> >> Fetch ftp://ftp.usa.openbsd.org/pub/OpenBSD/distfiles//hdf5-1.8.15-patch1.tar.gz
> hdf5-1.8.15-patch1.tar.gz: No such file or directory.
> >> Fetch http://ftp.fr.openbsd.org/pub/OpenBSD/distfiles//hdf5-1.8.15-patch1.tar.gz
> ftp: Error retrieving file: 404 Not Found
> *** Error 1 in /usr/ports/math/hdf5 (/usr/ports/infrastructure/mk/bsd.port.mk:2954 '/usr/ports/distfiles/hdf5-1.8.15-patch1.tar.gz': @lock=h...)
> *** Error 1 in /usr/ports/math/hdf5 (/usr/ports/infrastructure/mk/bsd.port.mk:2321 '_internal-fetch')
> *** Error 1 in /usr/ports/math/hdf5 (/usr/ports/infrastructure/mk/bsd.port.mk:2575 '/usr/ports/pobj/hdf5-1.8.15pl1/.extract_done')
> *** Error 1 in /usr/ports/math/hdf5 (/usr/ports/infrastructure/mk/bsd.port.mk:1952 '/usr/ports/packages/i386/all/hdf5-1.8.15pl1p0.tgz')
> *** Error 1 in /usr/ports/math/hdf5 (/usr/ports/infrastructure/mk/bsd.port.mk:2508 '_internal-package')
> *** Error 1 in /usr/ports/math/hdf5 (/usr/ports/infrastructure/mk/bsd.port.mk:2488 'package')
> *** Error 1 in /usr/ports/math/hdf5 (/usr/ports/infrastructure/mk/bsd.port.mk:1969 '/var/db/pkg/hdf5-1.8.15pl1p0/+CONTENTS')
> *** Error 1 in /usr/ports/math/hdf5 (/usr/ports/infrastructure/mk/bsd.port.mk:2488 'install')
> *** Error 1 in . (/usr/ports/infrastructure/mk/bsd.port.mk:2112 '/usr/ports/pobj/octave-4.0.0/.dep-math-hdf5')
> *** Error 1 in . (/usr/ports/infrastructure/mk/bsd.port.mk:2575 '/usr/ports/pobj/octave-4.0.0/.extract_done')
> *** Error 1 in . (/usr/ports/infrastructure/mk/bsd.port.mk:1952 '/usr/ports/packages/i386/all/octave-4.0.0.tgz')
> *** Error 1 in . (/usr/ports/infrastructure/mk/bsd.port.mk:2508 '_internal-package')
> *** Error 1 in . (/usr/ports/infrastructure/mk/bsd.port.mk:2488 'package')
> *** Error 1 in . (/usr/ports/infrastructure/mk/bsd.port.mk:1969 '/var/db/pkg/octave-4.0.0/+CONTENTS')
> *** Error 1 in /usr/ports/math/octave (/usr/ports/infrastructure/mk/bsd.port.mk:2488 'install')
>

Try this patch:

Index: Makefile
===================================================================
RCS file: /cvs/ports/math/hdf5/Makefile,v
retrieving revision 1.3
diff -u -p -r1.3 Makefile
--- Makefile 30 Jun 2015 09:15:32 -0000 1.3
+++ Makefile 18 Feb 2016 01:35:20 -0000
@@ -5,7 +5,7 @@ COMMENT = Hierarchical Data Format 5 Te
 V = 1.8.15-patch1
 DISTNAME = hdf5-${V}
 PKGNAME = hdf5-${V:S/-patch/pl/}
-REVISION = 0
+REVISION = 1
 
 SHARED_LIBS += hdf5 0.0 # 10.1
 SHARED_LIBS += hdf5_cpp 0.0 # 10.1
@@ -23,7 +23,8 @@ PERMIT_PACKAGE_CDROM = Yes
 
 WANTLIB += c m stdc++ z
 
-MASTER_SITES = http://www.hdfgroup.org/ftp/HDF5/current/src/
+MASTER_SITES = https://www.hdfgroup.org/ftp/HDF5/current/src/ \
+ https://www.hdfgroup.org/ftp/HDF5/releases/hdf5-${V}/src/
 
 SEPARATE_BUILD = Yes
 CONFIGURE_STYLE = gnu

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Re: [5.8-stable] math/hdf5

Stuart Henderson
On 2016/02/18 02:41, Juan Francisco Cantero Hurtado wrote:

>
> Index: Makefile
> ===================================================================
> RCS file: /cvs/ports/math/hdf5/Makefile,v
> retrieving revision 1.3
> diff -u -p -r1.3 Makefile
> --- Makefile 30 Jun 2015 09:15:32 -0000 1.3
> +++ Makefile 18 Feb 2016 01:35:20 -0000
> @@ -5,7 +5,7 @@ COMMENT = Hierarchical Data Format 5 Te
>  V = 1.8.15-patch1
>  DISTNAME = hdf5-${V}
>  PKGNAME = hdf5-${V:S/-patch/pl/}
> -REVISION = 0
> +REVISION = 1

bump isn't needed for a MASTER_SITES change

> -MASTER_SITES = http://www.hdfgroup.org/ftp/HDF5/current/src/
> +MASTER_SITES = https://www.hdfgroup.org/ftp/HDF5/current/src/ \
> + https://www.hdfgroup.org/ftp/HDF5/releases/hdf5-${V}/src/

it would make sense to do this for -current too, I think

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Re: [5.8-stable] math/hdf5

Adam Jensen
In reply to this post by Juan Francisco Cantero Hurtado
On Thu, 18 Feb 2016 02:41:54 +0100
Juan Francisco Cantero Hurtado <[hidden email]> wrote:

> On Wed, Feb 17, 2016 at 02:58:43PM -0500, Adam Jensen wrote:
> > ===> octave-4.0.0 depends on: hdf5-* - not found
> > ===>  Verifying install for hdf5-* in math/hdf5
> > ===>  Checking files for hdf5-1.8.15pl1p0
> > >> Fetch http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.15-patch1.tar.gz
> > ftp: Error retrieving file: 404 Not Found
> > >> Fetch http://ftp.openbsd.org/pub/OpenBSD/distfiles//hdf5-1.8.15-patch1.tar.gz
> > ftp: Error retrieving file: 404 Not Found
> > >> Fetch ftp://ftp.usa.openbsd.org/pub/OpenBSD/distfiles//hdf5-1.8.15-patch1.tar.gz
> > hdf5-1.8.15-patch1.tar.gz: No such file or directory.
> > >> Fetch http://ftp.fr.openbsd.org/pub/OpenBSD/distfiles//hdf5-1.8.15-patch1.tar.gz
> > ftp: Error retrieving file: 404 Not Found
> > *** Error 1 in /usr/ports/math/hdf5 (/usr/ports/infrastructure/mk/bsd.port.mk:2954 '/usr/ports/distfiles/hdf5-1.8.15-patch1.tar.gz': @lock=h...)
> > *** Error 1 in /usr/ports/math/hdf5 (/usr/ports/infrastructure/mk/bsd.port.mk:2321 '_internal-fetch')
> > *** Error 1 in /usr/ports/math/hdf5 (/usr/ports/infrastructure/mk/bsd.port.mk:2575 '/usr/ports/pobj/hdf5-1.8.15pl1/.extract_done')
> > *** Error 1 in /usr/ports/math/hdf5 (/usr/ports/infrastructure/mk/bsd.port.mk:1952 '/usr/ports/packages/i386/all/hdf5-1.8.15pl1p0.tgz')
> > *** Error 1 in /usr/ports/math/hdf5 (/usr/ports/infrastructure/mk/bsd.port.mk:2508 '_internal-package')
> > *** Error 1 in /usr/ports/math/hdf5 (/usr/ports/infrastructure/mk/bsd.port.mk:2488 'package')
> > *** Error 1 in /usr/ports/math/hdf5 (/usr/ports/infrastructure/mk/bsd.port.mk:1969 '/var/db/pkg/hdf5-1.8.15pl1p0/+CONTENTS')
> > *** Error 1 in /usr/ports/math/hdf5 (/usr/ports/infrastructure/mk/bsd.port.mk:2488 'install')
> > *** Error 1 in . (/usr/ports/infrastructure/mk/bsd.port.mk:2112 '/usr/ports/pobj/octave-4.0.0/.dep-math-hdf5')
> > *** Error 1 in . (/usr/ports/infrastructure/mk/bsd.port.mk:2575 '/usr/ports/pobj/octave-4.0.0/.extract_done')
> > *** Error 1 in . (/usr/ports/infrastructure/mk/bsd.port.mk:1952 '/usr/ports/packages/i386/all/octave-4.0.0.tgz')
> > *** Error 1 in . (/usr/ports/infrastructure/mk/bsd.port.mk:2508 '_internal-package')
> > *** Error 1 in . (/usr/ports/infrastructure/mk/bsd.port.mk:2488 'package')
> > *** Error 1 in . (/usr/ports/infrastructure/mk/bsd.port.mk:1969 '/var/db/pkg/octave-4.0.0/+CONTENTS')
> > *** Error 1 in /usr/ports/math/octave (/usr/ports/infrastructure/mk/bsd.port.mk:2488 'install')
> >
>
> Try this patch:
>
> Index: Makefile
> ===================================================================
> RCS file: /cvs/ports/math/hdf5/Makefile,v
> retrieving revision 1.3
> diff -u -p -r1.3 Makefile
> --- Makefile 30 Jun 2015 09:15:32 -0000 1.3
> +++ Makefile 18 Feb 2016 01:35:20 -0000
> @@ -5,7 +5,7 @@ COMMENT = Hierarchical Data Format 5 Te
>  V = 1.8.15-patch1
>  DISTNAME = hdf5-${V}
>  PKGNAME = hdf5-${V:S/-patch/pl/}
> -REVISION = 0
> +REVISION = 1
>  
>  SHARED_LIBS += hdf5 0.0 # 10.1
>  SHARED_LIBS += hdf5_cpp 0.0 # 10.1
> @@ -23,7 +23,8 @@ PERMIT_PACKAGE_CDROM = Yes
>  
>  WANTLIB += c m stdc++ z
>  
> -MASTER_SITES = http://www.hdfgroup.org/ftp/HDF5/current/src/
> +MASTER_SITES = https://www.hdfgroup.org/ftp/HDF5/current/src/ \
> + https://www.hdfgroup.org/ftp/HDF5/releases/hdf5-${V}/src/
>  
>  SEPARATE_BUILD = Yes
>  CONFIGURE_STYLE = gnu

Thanks, I used the link from your patch for this work around:

cd /usr/ports/distfiles
wget https://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.15-patch1/src/hdf5-1.8.15-patch1.tar.gz
cd /usr/ports/math/hdf5/
make install clean

Would your patch be the kind of thing that gets pushed into -stable updates? (and/or) Will an upcoming -stable update include a fix for /usr/ports/math/hdf5 (and other problems of this class)?

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Re: [5.8-stable] math/hdf5

Juan Francisco Cantero Hurtado
On Fri, Feb 19, 2016 at 05:27:07PM -0500, Adam Jensen wrote:
[...]
>
> Thanks, I used the link from your patch for this work around:
>
> cd /usr/ports/distfiles
> wget https://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.15-patch1/src/hdf5-1.8.15-patch1.tar.gz
> cd /usr/ports/math/hdf5/
> make install clean
>
> Would your patch be the kind of thing that gets pushed into -stable updates? (and/or) Will an upcoming -stable update include a fix for /usr/ports/math/hdf5 (and other problems of this class)?

Yes, I will commit the patch after of the cvs unlock. (late March, I guess)

--
Juan Francisco Cantero Hurtado http://juanfra.info

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