Re: [Fink-users] Build of octave-3.8.2-11 failed

[Alexander Hansen]

> On Dec 5, 2016, at 07:39, Alexander Hansen  
> wrote:
> 
> 
> 

> I didn’t notice the message on the 21st, sorry.  
> 
> “fink dumpinfo -finfofile ” will give you the correct path to 
> whatever .info file fink is actually using—this is particularly useful when 
> you’re using the local directory.  
> 
> One note:  Fink caches the .info file, so it’s possible that Gary might be 
> using the cached version.  Try using “fink index -f” to rebuild the cache.
> 
> 
> 

I just had a chance to make an update in the distribution.  The revision of the 
package remains unchanged.  

You can run “fink dumpinfo -fcompilescript octave” to dump the compile script 
and verify that “ac_cv_func_mkostemp=no” has been appended.

-- 
Alexander Hansen, Ph.D.
Fink User Liaison


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Re: [Fink-users] Build of octave-3.8.2-11 failed

[Alexander Hansen]

> On Dec 5, 2016, at 02:35, Jacques Bloch  wrote:
> 
> Dear Gary,
> 
> I submitted the same error report on Nov 21 but never got a reply. I was 
> aware that Homebrew had encountered the same error, but did not know how to 
> get around it with Fink, as I am not really an expert with the file structure 
> and build procedure of Fink. However, armed with your hint about where to 
> make the change suggested by Martin, I was able to get Octave to build. All I 
> did was indeed to replace line 251 in: 
> "/sw/fink/10.9-libcxx/stable/main/finkinfo/sci/octave-3.8.2.info 
> ” from
> ./configure %c
> to
> ./configure %c "ac_cv_func_mkostemp=no”
> 
> "fink update-all" then did the job properly and built octave 3.8.2-11.
> 
> Not sure why this does not work for you. Did you modify the current info 
> file? (I had trouble to find the info file at all).
> 
> Note: /sw/fink/dists is linked to /sw/fink/10.12 which is linked in turn to 
> /sw/fink/10.9-libcxx.
> 
> Good luck,
> Jacques
> 
> ---
> Dr. Jacques C.R. Bloch
> Institute for Theoretical Physics
> University of Regensburg
> 93040 Regensburg, Germany
> tel: +49 941 943-2018
> fax: +49 941 943-3887
> email: jacques.bl...@ur.de 
> web: http://homepages.uni-regensburg.de/~blj05290 
> 
> 
> 
> 
>> On 4 Dec 2016, at 22:56, Gary K. Olson > > wrote:
>> 
>> On Dec 4, 2016, at 2:04 PM MDT, Gary Olson > > replied: 
>> 
>>> On Dec 3, 2016, at 4:08 PM, Martin Costabel >> > wrote:
>> 
>> 
>>> This is a bug that homebrew and macports also have noticed, caused by the 
>>> new function mkostemp in Sierra that octave doesn't yet know about. Octave 
>>> uses its own stdlib.h that does not have this function. A workaround is to 
>>> run configure as
>> 
>>> 
>> 
>>> ./configure %c "ac_cv_func_mkostemp=no"
>> 
>>> 
>> 
>>> With this, it built for me (after I updated fink-package-precedence to the 
>>> latest version, anyway; with the older one that was installed it crashed at 
>>> the end due to an otool error.)
>> 
>>> 
>> 
>>> --
>> 
>>> Martin
>> 
>> I changed the ./configure line in octave-3.8.2-11.info 
>>  (line 251) as that seemed the proper place 
>> and reran the the build, but I got the same error message as before.  I seem 
>> to be using the newest fink-package-prededence (11/10/16 for info file and 
>> 11/20/16 for the patch). I ran the build again with one build job, but got 
>> same error. Here is build script from last compile before error:
>> 
>>> libtool: compile:  oct-cxx -DHAVE_CONFIG_H -I. -I../.. -I../../libgnu 
>>> -I../../libgnu -I/sw/include -I/sw/include/freetype2 -O3 -MD -D_THREAD_SAFE 
>>> -pthread -MT Faddeeva/libcruft_la-Faddeeva.lo -MD -MP -MF 
>>> Faddeeva/.deps/libcruft_la-Faddeeva.Tpo -c Faddeeva/Faddeeva.cc 
>>>   -fno-common -DPIC -o 
>>> Faddeeva/.libs/libcruft_la-Faddeeva.o
>>> In file included from Faddeeva/Faddeeva.cc:159 :
>>> In file included from Faddeeva/Faddeeva.hh:30:
>>> In file included from 
>>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/complex:247:
>>> In file included from 
>>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/sstream:174:
>>> In file included from 
>>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/ostream:140:
>>> In file included from 
>>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/locale:192:
>>> In file included from 
>>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdlib:86:
>>> ../../libgnu/stdlib.h:668:19: error: no member named 'mkostemp' in the 
>>> global namespace
>>> _GL_CXXALIAS_SYS (mkostemp, int, (char * /*template*/, int /*flags*/));
>>> ~~^~~~
>>> ../../libgnu/stdio.h:266:45: note: expanded from macro '_GL_CXXALIAS_SYS'
>>>   static rettype (*func) parameters = ::func;  \
>>>   ~~^
>>> 1 error generated.
>>> make[2]: *** [Faddeeva/libcruft_la-Faddeeva.lo] Error 1
>>> make[1]: *** [all-recursive] Error 1
>>> make: *** [all] Error 2
>>> ### execution of /tmp/fink.e0t0J failed, exit code 2
>>> ### execution of /tmp/fink.r32uz failed, exit code 2
>>> Removing runtime build-lock...
>>> Removing build-lock package...
>>> /sw/bin/dpkg-lockwait -r fink-buildlock-octave-3.8.2-11
>>> (Reading database ... 457004 files and directories currently installed.)
>>> Removing fink-buildlock-octave-3.8.2-11 ...
>>> Reading buildlock packages...
>>> /sw/bin/dpkg-lockwait -i 

Re: [Fink-users] Build of octave-3.8.2-11 failed

[Jacques Bloch]

Dear Gary,

I submitted the same error report on Nov 21 but never got a reply. I was aware 
that Homebrew had encountered the same error, but did not know how to get 
around it with Fink, as I am not really an expert with the file structure and 
build procedure of Fink. However, armed with your hint about where to make the 
change suggested by Martin, I was able to get Octave to build. All I did was 
indeed to replace line 251 in: 
"/sw/fink/10.9-libcxx/stable/main/finkinfo/sci/octave-3.8.2.info 
” from
./configure %c
to
./configure %c "ac_cv_func_mkostemp=no”

"fink update-all" then did the job properly and built octave 3.8.2-11.

Not sure why this does not work for you. Did you modify the current info file? 
(I had trouble to find the info file at all).

Note: /sw/fink/dists is linked to /sw/fink/10.12 which is linked in turn to 
/sw/fink/10.9-libcxx.

Good luck,
Jacques

---
Dr. Jacques C.R. Bloch
Institute for Theoretical Physics
University of Regensburg
93040 Regensburg, Germany
tel: +49 941 943-2018
fax: +49 941 943-3887
email: jacques.bl...@ur.de
web: http://homepages.uni-regensburg.de/~blj05290



> On 4 Dec 2016, at 22:56, Gary K. Olson  wrote:
> 
> On Dec 4, 2016, at 2:04 PM MDT, Gary Olson  > replied: 
> 
>> On Dec 3, 2016, at 4:08 PM, Martin Costabel > > wrote:
> 
> 
>> This is a bug that homebrew and macports also have noticed, caused by the 
>> new function mkostemp in Sierra that octave doesn't yet know about. Octave 
>> uses its own stdlib.h that does not have this function. A workaround is to 
>> run configure as
> 
>> 
> 
>> ./configure %c "ac_cv_func_mkostemp=no"
> 
>> 
> 
>> With this, it built for me (after I updated fink-package-precedence to the 
>> latest version, anyway; with the older one that was installed it crashed at 
>> the end due to an otool error.)
> 
>> 
> 
>> --
> 
>> Martin
> 
> I changed the ./configure line in octave-3.8.2-11.info 
>  (line 251) as that seemed the proper place and 
> reran the the build, but I got the same error message as before.  I seem to 
> be using the newest fink-package-prededence (11/10/16 for info file and 
> 11/20/16 for the patch). I ran the build again with one build job, but got 
> same error. Here is build script from last compile before error:
> 
>> libtool: compile:  oct-cxx -DHAVE_CONFIG_H -I. -I../.. -I../../libgnu 
>> -I../../libgnu -I/sw/include -I/sw/include/freetype2 -O3 -MD -D_THREAD_SAFE 
>> -pthread -MT Faddeeva/libcruft_la-Faddeeva.lo -MD -MP -MF 
>> Faddeeva/.deps/libcruft_la-Faddeeva.Tpo -c Faddeeva/Faddeeva.cc 
>>   -fno-common -DPIC -o 
>> Faddeeva/.libs/libcruft_la-Faddeeva.o
>> In file included from Faddeeva/Faddeeva.cc:159 :
>> In file included from Faddeeva/Faddeeva.hh:30:
>> In file included from 
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/complex:247:
>> In file included from 
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/sstream:174:
>> In file included from 
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/ostream:140:
>> In file included from 
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/locale:192:
>> In file included from 
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdlib:86:
>> ../../libgnu/stdlib.h:668:19: error: no member named 'mkostemp' in the 
>> global namespace
>> _GL_CXXALIAS_SYS (mkostemp, int, (char * /*template*/, int /*flags*/));
>> ~~^~~~
>> ../../libgnu/stdio.h:266:45: note: expanded from macro '_GL_CXXALIAS_SYS'
>>   static rettype (*func) parameters = ::func;  \
>>   ~~^
>> 1 error generated.
>> make[2]: *** [Faddeeva/libcruft_la-Faddeeva.lo] Error 1
>> make[1]: *** [all-recursive] Error 1
>> make: *** [all] Error 2
>> ### execution of /tmp/fink.e0t0J failed, exit code 2
>> ### execution of /tmp/fink.r32uz failed, exit code 2
>> Removing runtime build-lock...
>> Removing build-lock package...
>> /sw/bin/dpkg-lockwait -r fink-buildlock-octave-3.8.2-11
>> (Reading database ... 457004 files and directories currently installed.)
>> Removing fink-buildlock-octave-3.8.2-11 ...
>> Reading buildlock packages...
>> /sw/bin/dpkg-lockwait -i /sw/fink/debs/fort77_1.18-19_darwin-x86_64.deb
>> Selecting previously deselected package fort77.
>> (Reading database ... 457003 files and directories currently installed.)
>> Unpacking fort77 (from .../fort77_1.18-19_darwin-x86_64.deb) ...
>> Setting up fort77 (1.18-19) ...
>> 
>> Failed: phase compiling: octave-3.8.2-11 failed
> 

Re: [Fink-users] Build of octave-3.8.2-11 failed

[Martin Costabel]

On 4/12/16 22:56, Gary K. Olson wrote:
> On Dec 4, 2016, at 2:04 PM MDT, Gary Olson  > replied:
>
>> On Dec 3, 2016, at 4:08 PM, Martin Costabel > > wrote:
[]
>> ./configure %c "ac_cv_func_mkostemp=no"
>>
>> With this, it built for me (after I updated
[]
> I changed the ./configure line in octave-3.8.2-11.info
>  (line 251) as that seemed the proper place
> and reran the the build, but I got the same error message as before.  I
[]

Can you see the line

checking for mkostemp... (cached) no

in the configure output? Or does it say "... yes"?
If the latter, your change in the info file wasn't used, somehow.

-- 
Martin



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Re: [Fink-users] Build of octave-3.8.2-11 failed

[Gary K. Olson]

On Dec 4, 2016, at 2:04 PM MDT, Gary Olson > replied: 

> On Dec 3, 2016, at 4:08 PM, Martin Costabel  wrote:


> This is a bug that homebrew and macports also have noticed, caused by the new 
> function mkostemp in Sierra that octave doesn't yet know about. Octave uses 
> its own stdlib.h that does not have this function. A workaround is to run 
> configure as

> 

> ./configure %c "ac_cv_func_mkostemp=no"

> 

> With this, it built for me (after I updated fink-package-precedence to the 
> latest version, anyway; with the older one that was installed it crashed at 
> the end due to an otool error.)

> 

> --

> Martin

I changed the ./configure line in octave-3.8.2-11.info 
 (line 251) as that seemed the proper place and 
reran the the build, but I got the same error message as before.  I seem to be 
using the newest fink-package-prededence (11/10/16 for info file and 11/20/16 
for the patch). I ran the build again with one build job, but got same error. 
Here is build script from last compile before error:

> libtool: compile:  oct-cxx -DHAVE_CONFIG_H -I. -I../.. -I../../libgnu 
> -I../../libgnu -I/sw/include -I/sw/include/freetype2 -O3 -MD -D_THREAD_SAFE 
> -pthread -MT Faddeeva/libcruft_la-Faddeeva.lo -MD -MP -MF 
> Faddeeva/.deps/libcruft_la-Faddeeva.Tpo -c Faddeeva/Faddeeva.cc  -fno-common 
> -DPIC -o Faddeeva/.libs/libcruft_la-Faddeeva.o
> In file included from Faddeeva/Faddeeva.cc:159:
> In file included from Faddeeva/Faddeeva.hh:30:
> In file included from 
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/complex:247:
> In file included from 
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/sstream:174:
> In file included from 
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/ostream:140:
> In file included from 
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/locale:192:
> In file included from 
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdlib:86:
> ../../libgnu/stdlib.h:668:19: error: no member named 'mkostemp' in the global 
> namespace
> _GL_CXXALIAS_SYS (mkostemp, int, (char * /*template*/, int /*flags*/));
> ~~^~~~
> ../../libgnu/stdio.h:266:45: note: expanded from macro '_GL_CXXALIAS_SYS'
>   static rettype (*func) parameters = ::func;  \
>   ~~^
> 1 error generated.
> make[2]: *** [Faddeeva/libcruft_la-Faddeeva.lo] Error 1
> make[1]: *** [all-recursive] Error 1
> make: *** [all] Error 2
> ### execution of /tmp/fink.e0t0J failed, exit code 2
> ### execution of /tmp/fink.r32uz failed, exit code 2
> Removing runtime build-lock...
> Removing build-lock package...
> /sw/bin/dpkg-lockwait -r fink-buildlock-octave-3.8.2-11
> (Reading database ... 457004 files and directories currently installed.)
> Removing fink-buildlock-octave-3.8.2-11 ...
> Reading buildlock packages...
> /sw/bin/dpkg-lockwait -i /sw/fink/debs/fort77_1.18-19_darwin-x86_64.deb
> Selecting previously deselected package fort77.
> (Reading database ... 457003 files and directories currently installed.)
> Unpacking fort77 (from .../fort77_1.18-19_darwin-x86_64.deb) ...
> Setting up fort77 (1.18-19) ...
> 
> Failed: phase compiling: octave-3.8.2-11 failed

Any thoughts on what I am still doing wrong? 
Gary K Olson

My system info is:

Package manager version: 0.41.1
Distribution version: selfupdate-rsync Sun Dec  4 11:59:59 2016, 10.12, x86_64
Trees: local/main stable/main local/injected
Xcode.app: 8.1
Xcode command-line tools: 8.1.0.0.1.1476494586
Max. Fink build jobs:  1


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Re: [Fink-users] Build of octave-3.8.2-11 failed

[Martin Costabel]

On 3/12/16 07:51, Alexander Hansen wrote:
>
>> On Dec 2, 2016, at 21:02, Gary K. Olson > > wrote:
>>
>> I was compiling octave-3.8.2-11, and the build failed after not
>> finding *member named 'mkostemp' in the global namespace.* Not sure
>> that missing member is error but recursive errors did occur while
>> compiling lapack-xtra/*.f files. Here is build script of that portion:
[]
>> 
>> Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdlib:86:
>> *../../libgnu/stdlib.h:668:19: **error: **no member named
>> 'mkostemp' in the global namespace*
>> _GL_CXXALIAS_SYS (mkostemp, int, (char * /*template*/, int
>> /*flags*/));
>> *~~^~~~*
>> *../../libgnu/stdio.h:266:45: **note: *expanded from macro
>> '_GL_CXXALIAS_SYS'
>>   static rettype (*func) parameters = ::func;  \
[]...
>>
>> Failed: phase compiling: octave-3.8.2-11 failed
>>
>> My system info is:
>>
>> Package manager version: 0.41.1
>> Distribution version: selfupdate-rsync Fri Dec  2 20:05:59 2016,
>> 10.12, x86_64
>> Trees: local/main stable/main local/injected
>> Xcode.app: 8.1
>> Xcode command-line tools: 8.1.0.0.1.1476494586
>> Max. Fink build jobs:  4
>>
>> Any help would be appreciated. Thank you.
>>
>> Gary K Olson
>
> Please try again, using a single build job, and post starting with the
> entire line of output just before the first error message.  Errors with
> multiple jobs are harder to track down.

This is a bug that homebrew and macports also have noticed, caused by 
the new function mkostemp in Sierra that octave doesn't yet know about. 
Octave uses its own stdlib.h that does not have this function. A 
workaround is to run configure as

  ./configure %c "ac_cv_func_mkostemp=no"

With this, it built for me (after I updated fink-package-precedence to 
the latest version, anyway; with the older one that was installed it 
crashed at the end due to an otool error.)

-- 
Martin

--
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Re: [Fink-users] Build of octave-3.8.2-11 failed

[Alexander Hansen]

> On Dec 2, 2016, at 21:02, Gary K. Olson  wrote:
> 
> I was compiling octave-3.8.2-11, and the build failed after not finding 
> member named 'mkostemp' in the global namespace. Not sure that missing member 
> is error but recursive errors did occur while compiling lapack-xtra/*.f 
> files. Here is build script of that portion:
> 
> In file included from /Applications//bin/sh ../../libtool  --tag=F77   
> --mode=compile /sw/bin/gfortran-fsf-5  -O3 -ff2c -c -o 
> lapack-xtra/libcruft_la-xslange.lo `test -f 'lapack-xtra/xslange.f' || echo 
> './'`lapack-xtra/xslange.f
> libtool: compile:  /sw/bin/gfortran-fsf-5 -O3 -ff2c -c lapack-xtra/xilaenv.f  
> -fno-common -o lapack-xtra/.libs/libcruft_la-xilaenv.o
> Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdlib:86:
> ../../libgnu/stdlib.h:668:19: error: no member named 'mkostemp' in the global 
> namespace
> _GL_CXXALIAS_SYS (mkostemp, int, (char * /*template*/, int /*flags*/));
> ~~^~~~
> ../../libgnu/stdio.h:266:45: note: expanded from macro '_GL_CXXALIAS_SYS'
>   static rettype (*func) parameters = ::func;  \
>   ~~^
> libtool: compile:  /sw/bin/gfortran-fsf-5 -O3 -ff2c -c lapack-xtra/xslamch.f  
> -fno-common -o lapack-xtra/.libs/libcruft_la-xslamch.o
> /bin/sh ../../libtool  --tag=F77   --mode=compile /sw/bin/gfortran-fsf-5  -O3 
> -ff2c -c -o lapack-xtra/libcruft_la-xzlange.lo `test -f 
> 'lapack-xtra/xzlange.f' || echo './'`lapack-xtra/xzlange.f
> /bin/sh ../../libtool  --tag=F77   --mode=compile /sw/bin/gfortran-fsf-5  -O3 
> -ff2c -c -o lapack-xtra/libcruft_la-zrsf2csf.lo `test -f 
> 'lapack-xtra/zrsf2csf.f' || echo './'`lapack-xtra/zrsf2csf.f
> 1 error generated.
> make[2]: *** [Faddeeva/libcruft_la-Faddeeva.lo] Error 1
> make[2]: *** Waiting for unfinished jobs
> libtool: compile:  /sw/bin/gfortran-fsf-5 -O3 -ff2c -c lapack-xtra/xslange.f  
> -fno-common -o lapack-xtra/.libs/libcruft_la-xslange.o
> libtool: compile:  /sw/bin/gfortran-fsf-5 -O3 -ff2c -c lapack-xtra/xzlange.f  
> -fno-common -o lapack-xtra/.libs/libcruft_la-xzlange.o
> libtool: compile:  /sw/bin/gfortran-fsf-5 -O3 -ff2c -c lapack-xtra/zrsf2csf.f 
>  -fno-common -o lapack-xtra/.libs/libcruft_la-zrsf2csf.o
> make[1]: *** [all-recursive] Error 1
> make: *** [all] Error 2
> ### execution of /tmp/fink.Kd447 failed, exit code 2
> ### execution of /tmp/fink.TR9Qp failed, exit code 2
> Removing runtime build-lock...
> Removing build-lock package...
> /sw/bin/dpkg-lockwait -r fink-buildlock-octave-3.8.2-11
> (Reading database ... 457001 files and directories currently installed.)
> Removing fink-buildlock-octave-3.8.2-11 ...
> Reading buildlock packages...
> /sw/bin/dpkg-lockwait -i /sw/fink/debs/fort77_1.18-19_darwin-x86_64.deb
> Selecting previously deselected package fort77.
> (Reading database ... 457000 files and directories currently installed.)
> Unpacking fort77 (from .../fort77_1.18-19_darwin-x86_64.deb) ...
> Setting up fort77 (1.18-19) ...
> 
> Failed: phase compiling: octave-3.8.2-11 failed
> 
> My system info is:
> 
> Package manager version: 0.41.1
> Distribution version: selfupdate-rsync Fri Dec  2 20:05:59 2016, 10.12, x86_64
> Trees: local/main stable/main local/injected
> Xcode.app: 8.1
> Xcode command-line tools: 8.1.0.0.1.1476494586
> Max. Fink build jobs:  4
> 
> Any help would be appreciated. Thank you.
> 
> Gary K Olson

Please try again, using a single build job, and post starting with the entire 
line of output just before the first error message.  Errors with multiple jobs 
are harder to track down.

-- 
Alexander Hansen, Ph.D.
Fink User Liaison

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