subject:"Re\: \[Fink\-users\] Error in installing guile20"

Re: [Fink-users] Error in installing guile20

2016-10-03 Thread Alan

Thanks for the explanation!

Alan

On 3 October 2016 at 18:23, Derek Homeier <
de...@astro.physik.uni-goettingen.de> wrote:

> Hi Alan,
>
> On 2 Oct 2016, at 9:03 pm, Alan  wrote:
> >
> > Weird, I used Jack's files and it worked on Sierra. Fighting now to get
> openssl (another email submitted).
>
> the patch failure seemed to be related to a broken installation of the
> Command Line Tools,
> fixed after I redid the OS update to Sierra (discussed offline with Jack).
> With the clean 10.12 CLT the patch works, but Jack’s alternative
> suggestion to configure with
> ac_cv_func_clock_gettime=no solves the build failure as well.
>
> Cheers,
> Derek
>
>
>


-- 
Alan Wilter SOUSA da SILVA, DSc
Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588
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Re: [Fink-users] Error in installing guile20

2016-10-03 Thread Derek Homeier

Hi Alan,

On 2 Oct 2016, at 9:03 pm, Alan  wrote:
> 
> Weird, I used Jack's files and it worked on Sierra. Fighting now to get 
> openssl (another email submitted).

the patch failure seemed to be related to a broken installation of the Command 
Line Tools,
fixed after I redid the OS update to Sierra (discussed offline with Jack).
With the clean 10.12 CLT the patch works, but Jack’s alternative suggestion to 
configure with
ac_cv_func_clock_gettime=no solves the build failure as well.

Cheers,
Derek

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Re: [Fink-users] Error in installing guile20

2016-10-02 Thread Alan

Weird, I used Jack's files and it worked on Sierra. Fighting now to get
openssl (another email submitted).

Many thanks,

Alan

On 1 October 2016 at 02:41, Derek Homeier <
de...@astro.physik.uni-goettingen.de> wrote:

> Jack,
>
> > On 30 Sep 2016, at 8:23 pm, Jack Howarth 
> wrote:
> >
> > Does the attached guile20 packaging for the 2.0.12 release work?
> Both MacPorts and Homebrew are building on Sierra with the same patch using
> the 2.0.12 release.
> > Jack
> > ps This packaging works fine here on El Capitan with Xcode 8.1 beta
> (don't have hardware for Sierra).
> >
> got my MacBook upgraded to Sierra now, and now the build in fact defaults
> to ac_cv_func_clock_gettime=yes,
> which fails again with
>
>   CC   libguile_2.0_la-stime.lo
> ../../libguile/stime.c:119:3: warning: implicit declaration of function
> 'clock_gettime' is invalid in C99 [-Wimplicit-function-declaration]
>   clock_gettime (CLOCK_REALTIME, );
>   ^
> ../../libguile/stime.c:119:18: error: use of undeclared identifier
> 'CLOCK_REALTIME'
>   clock_gettime (CLOCK_REALTIME, );
>  ^
> ../../libguile/stime.c:828:22: error: use of undeclared identifier
> 'CLOCK_REALTIME'
>   if (clock_gettime (CLOCK_REALTIME, _real_time_base) == 0)
>
> Adding ac_cv_func_clock_gettime=no to ConfigParams instead lets the build
> succeed.
> I am a bit confused about my Xcode installation now, though, because after
> the failure
> with the first variant fink tells me:
>
> Also include the following system information:
> Package manager version: 0.41.0
> Distribution version: selfupdate-rsync Fri Sep 30 23:54:16 2016, 10.12,
> x86_64
> Trees: stable/main local/main local/injected unstable/main
> Xcode.app: 8.0
> Xcode command-line tools: 7.3.1.0.1.1461711523
> Max. Fink build jobs:  1
>
> However according to AppStore I have installed both the update to
> “Command Line Tools (OS X 10.11) for Xcode Version 7.3” and
> “Command Line Tools (macOS Sierra version 10.12) for Xcode Version 8.0”
>
> and gcc -v
> Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr
> --with-gxx-include-dir=/usr/include/c++/4.2.1
> Apple LLVM version 8.0.0 (clang-800.0.38)
>
> xcode-select does not offer any useful options here.
>
> I should perhaps also note that updating llvm-gcc42 failed with this
> rather nondescriptive error:
>
> Adding multilib support to Makefile in /scratch.noindex/fink.build/
> llvm-gcc42-2336.11-37/objroot/src/libiberty
> with_multisubdir=i386
> make[2]: *** [all] Error 2
> + exit 1
> make[1]: *** [llvmgcc42] Error 1
> make: *** [install] Error 2
>
>
> Anyway, with just the modified ConfigParams guile20 seems to work both on
> El Capitan and Sierra,
> and I was also able to rebuild ffmpeg with the new guile20 installed…
>
> Cheers,
> Derek
> >
> > On Fri, Sep 30, 2016 at 10:30 AM, Derek Homeier  goettingen.de> wrote:
> > On 30 Sep 2016, at 12:02 pm, Alan  wrote:
> > >
> > > Well, I gave a try, I copied from stable to local and appended
> > >
> > > /sw/fink/dists/local/main/finkinfo/languages/guile20.patch
> > >
> > > with lines from https://gist.github.com/rahulg/
> baa500e84136f0965e9ade2fb36b90ba
> > >
> > > but, alas, it didn't work.
> > >
> > That patch file is outdated and no longer used; you'd need to replace it
> completely with the new
> > patch and then modify the info file to use it again in the internal
> patch script it is using now.
> > But note that this issue has been discussed on the list before:
> >
> > > On 15 Aug 2016, at 8:35 pm, Jack Howarth 
> wrote:
> > >
> > > Alternatively, rather than applying that ugly unreviewed patch, we
> could probably just pass ac_cv_func_clock_gettime=no to configure to avoid
> the new system calls until upstream catches up with the deviations in the
> Mac OS X implementation.
> > >Jack
>
>


-- 
Alan Wilter SOUSA da SILVA, DSc
Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588
--
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Re: [Fink-users] Error in installing guile20

2016-09-30 Thread Derek Homeier

Jack,

> On 30 Sep 2016, at 8:23 pm, Jack Howarth  wrote:
> 
> Does the attached guile20 packaging for the 2.0.12 release work? Both 
> MacPorts and Homebrew are building on Sierra with the same patch using the 
> 2.0.12 release.
> Jack
> ps This packaging works fine here on El Capitan with Xcode 8.1 beta (don't 
> have hardware for Sierra).
> 
got my MacBook upgraded to Sierra now, and now the build in fact defaults to 
ac_cv_func_clock_gettime=yes,
which fails again with

  CC   libguile_2.0_la-stime.lo
../../libguile/stime.c:119:3: warning: implicit declaration of function 
'clock_gettime' is invalid in C99 [-Wimplicit-function-declaration]
  clock_gettime (CLOCK_REALTIME, );
  ^
../../libguile/stime.c:119:18: error: use of undeclared identifier 
'CLOCK_REALTIME'
  clock_gettime (CLOCK_REALTIME, );
 ^
../../libguile/stime.c:828:22: error: use of undeclared identifier 
'CLOCK_REALTIME'
  if (clock_gettime (CLOCK_REALTIME, _real_time_base) == 0)

Adding ac_cv_func_clock_gettime=no to ConfigParams instead lets the build 
succeed.
I am a bit confused about my Xcode installation now, though, because after the 
failure
with the first variant fink tells me:

Also include the following system information:
Package manager version: 0.41.0
Distribution version: selfupdate-rsync Fri Sep 30 23:54:16 2016, 10.12, x86_64
Trees: stable/main local/main local/injected unstable/main
Xcode.app: 8.0
Xcode command-line tools: 7.3.1.0.1.1461711523
Max. Fink build jobs:  1

However according to AppStore I have installed both the update to 
“Command Line Tools (OS X 10.11) for Xcode Version 7.3” and
“Command Line Tools (macOS Sierra version 10.12) for Xcode Version 8.0”

and gcc -v  
   
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr 
--with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 8.0.0 (clang-800.0.38)

xcode-select does not offer any useful options here.

I should perhaps also note that updating llvm-gcc42 failed with this rather 
nondescriptive error:

Adding multilib support to Makefile in 
/scratch.noindex/fink.build/llvm-gcc42-2336.11-37/objroot/src/libiberty
with_multisubdir=i386
make[2]: *** [all] Error 2
+ exit 1
make[1]: *** [llvmgcc42] Error 1
make: *** [install] Error 2


Anyway, with just the modified ConfigParams guile20 seems to work both on El 
Capitan and Sierra,
and I was also able to rebuild ffmpeg with the new guile20 installed…

Cheers,
Derek
> 
> On Fri, Sep 30, 2016 at 10:30 AM, Derek Homeier 
>  wrote:
> On 30 Sep 2016, at 12:02 pm, Alan  wrote:
> >
> > Well, I gave a try, I copied from stable to local and appended
> >
> > /sw/fink/dists/local/main/finkinfo/languages/guile20.patch
> >
> > with lines from 
> > https://gist.github.com/rahulg/baa500e84136f0965e9ade2fb36b90ba
> >
> > but, alas, it didn't work.
> >
> That patch file is outdated and no longer used; you'd need to replace it 
> completely with the new
> patch and then modify the info file to use it again in the internal patch 
> script it is using now.
> But note that this issue has been discussed on the list before:
> 
> > On 15 Aug 2016, at 8:35 pm, Jack Howarth  wrote:
> >
> > Alternatively, rather than applying that ugly unreviewed patch, we could 
> > probably just pass ac_cv_func_clock_gettime=no to configure to avoid the 
> > new system calls until upstream catches up with the deviations in the Mac 
> > OS X implementation.
> >Jack



guile20.info
Description: Binary data
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Re: [Fink-users] Error in installing guile20

2016-09-30 Thread Derek Homeier

On 30 Sep 2016, at 5:46 pm, Alexander Hansen  
wrote:
> 
>> So you might first try to add the above definition to ConfigureParams (see 
>> attached .info); however I found
>> on Yosemite that ac_cv_func_clock_gettime=no is already set by default (see 
>> build/config.log in the package
>> build dir how it’s set on your system).
>> So if that does not work, you’d have to uncomment the PatchFile*, and in the 
>> PatchScript the %{default_script},
>> lines in the .info file if you wish to test that patch under Sierra. It does 
>> compile under Yosemite and passes all
>> tests except one (the same failure shows up with the standard setup), but I 
>> cannot tell if it resolves the problem
>> under 10.12...
>> 
>> HTH
>>  Derek
>> 
>> ———
> 
> If you want to set ac_cv_func_clock_getttime, you can try doing that in 
> guile20’s CompileScript by changing
> 
> ../configure %c
> 
> to
> 
> ac_cv_func_clock_gettime=no ../configure %c
> 
> (no guarantees that it works—I haven’t had a chance to try it on Sierra).
> 
In the info file I had attached I had added it to ConfigureParams, which works 
the same afaict.
But on Yosemite that’s already the automatic setting; if I force it instead to 
ac_cv_func_clock_gettime=yes
the build fails then in a different step on

  CC   libguile_2.0_la-stime.lo
../../libguile/stime.c:123:3: warning: implicit declaration of function 
'clock_gettime' is invalid in C99 [-Wimplicit-function-declaration]
  clock_gettime (CLOCK_REALTIME, );
  ^
../../libguile/stime.c:123:18: error: use of undeclared identifier 
'CLOCK_REALTIME'
  clock_gettime (CLOCK_REALTIME, );
 ^
../../libguile/stime.c:832:22: error: use of undeclared identifier 
'CLOCK_REALTIME'
  if (clock_gettime (CLOCK_REALTIME, _real_time_base) == 0)
 ^

so I am a bit sceptical if this will really fix it on Sierra…

Cheers,
Derek


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Re: [Fink-users] Error in installing guile20

2016-09-30 Thread Alexander Hansen


> On Sep 30, 2016, at 07:30, Derek Homeier 
>  wrote:
> 
> On 30 Sep 2016, at 12:02 pm, Alan  wrote:
>> 
>> Well, I gave a try, I copied from stable to local and appended 
>> 
>> /sw/fink/dists/local/main/finkinfo/languages/guile20.patch
>> 
>> with lines from 
>> https://gist.github.com/rahulg/baa500e84136f0965e9ade2fb36b90ba
>> 
>> but, alas, it didn't work.
>> 
> That patch file is outdated and no longer used; you'd need to replace it 
> completely with the new
> patch and then modify the info file to use it again in the internal patch 
> script it is using now.
> But note that this issue has been discussed on the list before:
> 
>> On 15 Aug 2016, at 8:35 pm, Jack Howarth  wrote:
>> 
>> Alternatively, rather than applying that ugly unreviewed patch, we could 
>> probably just pass ac_cv_func_clock_gettime=no to configure to avoid the new 
>> system calls until upstream catches up with the deviations in the Mac OS X 
>> implementation.
>>   Jack
>> 
>> On Mon, Aug 15, 2016 at 1:22 PM, Jack Howarth  
>> wrote:
>> The build issue for guile20 (and I assume also guile18) on 10.12 is 
>> described in...
>> 
>> http://lists.gnu.org/archive/html/bug-guile/2016-06/msg00252.html
>> 
>> and a hack to work around it proposed at...
>> 
>> https://gist.github.com/rahulg/baa500e84136f0965e9ade2fb36b90ba
>> 
> So you might first try to add the above definition to ConfigureParams (see 
> attached .info); however I found
> on Yosemite that ac_cv_func_clock_gettime=no is already set by default (see 
> build/config.log in the package
> build dir how it’s set on your system).
> So if that does not work, you’d have to uncomment the PatchFile*, and in the 
> PatchScript the %{default_script},
> lines in the .info file if you wish to test that patch under Sierra. It does 
> compile under Yosemite and passes all
> tests except one (the same failure shows up with the standard setup), but I 
> cannot tell if it resolves the problem
> under 10.12...
> 
> HTH
>   Derek
> 
> ———

If you want to set ac_cv_func_clock_getttime, you can try doing that in 
guile20’s CompileScript by changing

../configure %c

to

ac_cv_func_clock_gettime=no ../configure %c

(no guarantees that it works—I haven’t had a chance to try it on Sierra).

—Akh


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Re: [Fink-users] Error in installing guile20

2016-09-30 Thread Derek Homeier

On 30 Sep 2016, at 12:02 pm, Alan  wrote:
> 
> Well, I gave a try, I copied from stable to local and appended 
> 
> /sw/fink/dists/local/main/finkinfo/languages/guile20.patch
> 
> with lines from 
> https://gist.github.com/rahulg/baa500e84136f0965e9ade2fb36b90ba
> 
> but, alas, it didn't work.
> 
That patch file is outdated and no longer used; you'd need to replace it 
completely with the new
patch and then modify the info file to use it again in the internal patch 
script it is using now.
But note that this issue has been discussed on the list before:

> On 15 Aug 2016, at 8:35 pm, Jack Howarth  wrote:
> 
> Alternatively, rather than applying that ugly unreviewed patch, we could 
> probably just pass ac_cv_func_clock_gettime=no to configure to avoid the new 
> system calls until upstream catches up with the deviations in the Mac OS X 
> implementation.
>Jack
> 
> On Mon, Aug 15, 2016 at 1:22 PM, Jack Howarth  
> wrote:
> The build issue for guile20 (and I assume also guile18) on 10.12 is described 
> in...
> 
> http://lists.gnu.org/archive/html/bug-guile/2016-06/msg00252.html
> 
> and a hack to work around it proposed at...
> 
> https://gist.github.com/rahulg/baa500e84136f0965e9ade2fb36b90ba
> 
So you might first try to add the above definition to ConfigureParams (see 
attached .info); however I found
on Yosemite that ac_cv_func_clock_gettime=no is already set by default (see 
build/config.log in the package
build dir how it’s set on your system).
So if that does not work, you’d have to uncomment the PatchFile*, and in the 
PatchScript the %{default_script},
lines in the .info file if you wish to test that patch under Sierra. It does 
compile under Yosemite and passes all
tests except one (the same failure shows up with the standard setup), but I 
cannot tell if it resolves the problem
under 10.12...

HTH
Derek



guile20.info
Description: Binary data


guile20.patch
Description: Binary data
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Re: [Fink-users] Error in installing guile20

2016-09-30 Thread Alan

Well, I gave a try, I copied from stable to local and appended

/sw/fink/dists/local/main/finkinfo/languages/guile20.patch

with lines from https://gist.github.com/rahulg/
baa500e84136f0965e9ade2fb36b90ba

but, alas, it didn't work.

Alan

On 30 September 2016 at 09:18, Alan  wrote:

> Hi there,
>
> Same problem here. I know Fink has ways of patching files ... if pointed
> how to do this, I can give a try.
>
> Thanks,
>
> Alan
>
> On 29 September 2016 at 16:41, Joakim Kjellsson <
> joakim.kjells...@gmail.com> wrote:
>
>> Hi
>>
>> I’ve been trying to install ffmpeg via fink, which requires guile20.
>> However, I run into the following error:
>>
>> */usr/include/stdio.h:277:7: **note: *'tmpnam' has been explicitly
>> marked deprecated here
>> char*tmpnam(char *);
>> * ^*
>> 1 warning generated.
>>   CC   libguile_2.0_la-net_db.lo
>>   CC   libguile_2.0_la-socket.lo
>>   CC   libguile_2.0_la-regex-posix.lo
>>   CCLD libguile-2.0.la
>> Undefined symbols for architecture x86_64:
>>   "_clock_getcpuclockid", referenced from:
>>   _scm_init_stime in libguile_2.0_la-stime.o
>> ld: symbol(s) not found for architecture x86_64
>> clang: *error: *linker command failed with exit code 1 (use -v to see
>> invocation)
>> make[3]: *** [libguile-2.0.la] Error 1
>> make[2]: *** [all] Error 2
>>
>> The specs are the following:
>> Package manager version: 0.41.0
>> Distribution version: selfupdate-rsync Thu Sep 29 16:16:58 2016, 10.12,
>> x86_64
>> Trees: local/main stable/main
>> Xcode.app: 8.0
>> Xcode command-line tools: 8.0.0.0.1.1472435881
>> Max. Fink build jobs:  1
>>
>> After some time on google I found that the bug is because Apple have
>> changed something in a “clock” routine and that this patch
>> https://gist.github.com/rahulg/baa500e84136f0965e9ade2fb36b90ba
>> fixes it.
>> However, I have no idea where to put this fix or if it could be put into
>> the main version on fink.
>> Any help here is much appreciated.
>>
>> All the best
>> Joakim
>>
>> 
>> --
>>
>> ___
>> Fink-users mailing list
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>>
>
>
> --
> Alan Wilter SOUSA da SILVA, DSc
> Senior Bioinformatician, UniProt
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
> Tel: +44 (0)1223 494588
>



-- 
Alan Wilter SOUSA da SILVA, DSc
Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588
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Re: [Fink-users] Error in installing guile20

2016-09-30 Thread Alan

Hi there,

Same problem here. I know Fink has ways of patching files ... if pointed
how to do this, I can give a try.

Thanks,

Alan

On 29 September 2016 at 16:41, Joakim Kjellsson 
wrote:

> Hi
>
> I’ve been trying to install ffmpeg via fink, which requires guile20.
> However, I run into the following error:
>
> */usr/include/stdio.h:277:7: **note: *'tmpnam' has been explicitly marked
> deprecated here
> char*tmpnam(char *);
> * ^*
> 1 warning generated.
>   CC   libguile_2.0_la-net_db.lo
>   CC   libguile_2.0_la-socket.lo
>   CC   libguile_2.0_la-regex-posix.lo
>   CCLD libguile-2.0.la
> Undefined symbols for architecture x86_64:
>   "_clock_getcpuclockid", referenced from:
>   _scm_init_stime in libguile_2.0_la-stime.o
> ld: symbol(s) not found for architecture x86_64
> clang: *error: *linker command failed with exit code 1 (use -v to see
> invocation)
> make[3]: *** [libguile-2.0.la] Error 1
> make[2]: *** [all] Error 2
>
> The specs are the following:
> Package manager version: 0.41.0
> Distribution version: selfupdate-rsync Thu Sep 29 16:16:58 2016, 10.12,
> x86_64
> Trees: local/main stable/main
> Xcode.app: 8.0
> Xcode command-line tools: 8.0.0.0.1.1472435881
> Max. Fink build jobs:  1
>
> After some time on google I found that the bug is because Apple have
> changed something in a “clock” routine and that this patch
> https://gist.github.com/rahulg/baa500e84136f0965e9ade2fb36b90ba
> fixes it.
> However, I have no idea where to put this fix or if it could be put into
> the main version on fink.
> Any help here is much appreciated.
>
> All the best
> Joakim
>
> 
> --
>
> ___
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>


-- 
Alan Wilter SOUSA da SILVA, DSc
Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588
--
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Re: [Fink-users] Error in installing guile20

Re: [Fink-users] Error in installing guile20

Re: [Fink-users] Error in installing guile20

Re: [Fink-users] Error in installing guile20

Re: [Fink-users] Error in installing guile20

Re: [Fink-users] Error in installing guile20

Re: [Fink-users] Error in installing guile20

Re: [Fink-users] Error in installing guile20

Re: [Fink-users] Error in installing guile20

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