[GenABEL-dev] LATEX error on autoreconf
L.C. Karssen
lennart at karssen.org
Mon Oct 27 14:20:04 CET 2014
On 27-10-14 13:24, Frank, Alvaro Jesus wrote:
> How do I add the MPI .m4 file to autoconf without modifying the configure.ac?
If you installed the macros from the Debian/Ubuntu package no further
work is needed (at least it worked out of the box for me, Ubuntu 14.04).
The package installs the ax_* scripts in /usr/share/aclocal.
Alternatively, assuming the path to ax_prog_cxx_mpi.m4 is /my/m4/path,
you can run autoreconf like this:
autoreconf -i -I/my/m4/path
Lennart.
>
> http://stackoverflow.com/questions/5298830/how-to-include-m4-files-in-autoconf
>
> -Alvaro
> ________________________________________
> From: L.C. Karssen [lennart at karssen.org]
> Sent: Monday, October 27, 2014 1:13 PM
> To: Frank, Alvaro Jesus; genabel-devel at lists.r-forge.r-project.org
> Subject: Re: [GenABEL-dev] LATEX error on autoreconf
>
> Hi Alvaro,
>
> On 27-10-14 13:03, Frank, Alvaro Jesus wrote:
>> More on the problem, If I use autoreconf -fi it wont work, if I use autoreconf -i :
>>
>>
>> alvaro.frank@:/opt/omicabelnomm/OmicABELnoMM> autoreconf -i
>> configure.ac:6: installing `./install-sh'
>> configure.ac:6: installing `./missing'
>> Makefile.am: installing `./depcomp'
>> alvaro.frank@:/opt/omicabelnomm/OmicABELnoMM> ./configure
>> checking for a BSD-compatible install... /usr/bin/install -c
>> checking whether build environment is sane... yes
>> checking for a thread-safe mkdir -p... /bin/mkdir -p
>> checking for gawk... gawk
>> checking whether make sets $(MAKE)... yes
>> checking whether to disable maintainer-specific portions of Makefiles... yes
>> ./configure: line 3045: syntax error near unexpected token `test'
>> ./configure: line 3045: `AX_PROG_CXX_MPI(test "x$with_mpi" != "xno",'
>>
>
> That's weird... Indeed I didn't use the -f flag... But if I do (on a
> fresh checkout), it works without problems (I do have a 64 bit kernel):
>
> lennart at barabas /tmp
> ╰─$ svn checkout
> svn+ssh://lckarssen@svn.r-forge.r-project.org/svnroot/genabel/pkg/OmicABELnoMM
>
> A OmicABELnoMM/OmicOUT
> A OmicABELnoMM/OmicOUT/main.cpp
> A OmicABELnoMM/AUTHORS
> A OmicABELnoMM/ChangeLog
> A OmicABELnoMM/src
> A OmicABELnoMM/src/AIOwrapper.h
> A OmicABELnoMM/src/Definitions.h
> A OmicABELnoMM/src/Utility.cpp
> A OmicABELnoMM/src/main.cpp
> A OmicABELnoMM/src/Algorithm.cpp
> A OmicABELnoMM/src/Utility.h
> A OmicABELnoMM/src/AIOwrapper.cpp
> A OmicABELnoMM/src/Algorithm.h
> A OmicABELnoMM/compile
> A OmicABELnoMM/libs
> A OmicABELnoMM/libs/include
> A OmicABELnoMM/libs/lib
> A OmicABELnoMM/README
> A OmicABELnoMM/tests
> A OmicABELnoMM/tests/test.cpp
> A OmicABELnoMM/tests/Makefile.am
> A OmicABELnoMM/configure.ac
> A OmicABELnoMM/doc
> A OmicABELnoMM/doc/howtocompile.txt
> A OmicABELnoMM/doc/UserGuide.tex
> A OmicABELnoMM/INSTALL
> A OmicABELnoMM/COPYING
> A OmicABELnoMM/test-driver
> A OmicABELnoMM/Makefile.am
> A OmicABELnoMM/NEWS
> A OmicABELnoMM/examples
> A OmicABELnoMM/examples/XL.fvd
> A OmicABELnoMM/examples/results
> A OmicABELnoMM/examples/exclude_individuals.txt
> A OmicABELnoMM/examples/interactions
> A OmicABELnoMM/examples/interactions/INTR0.fvi
> A OmicABELnoMM/examples/interactions/INT11.fvi
> A OmicABELnoMM/examples/interactions/INTR1.fvi
> A OmicABELnoMM/examples/interactions/INTRR.fvi
> A OmicABELnoMM/examples/interactions/Y.fvd
> A OmicABELnoMM/examples/interactions/INT0.fvd
> A OmicABELnoMM/examples/interactions/INT1.fvd
> A OmicABELnoMM/examples/interactions/INTR.fvd
> A OmicABELnoMM/examples/interactions/INT011.fvd
> A OmicABELnoMM/examples/interactions/Y.fvi
> A OmicABELnoMM/examples/interactions/INT01R.fvd
> A OmicABELnoMM/examples/interactions/INT0.fvi
> A OmicABELnoMM/examples/interactions/INT1RR.fvd
> A OmicABELnoMM/examples/interactions/INT1.fvi
> A OmicABELnoMM/examples/interactions/INTR.fvi
> A OmicABELnoMM/examples/interactions/INT011.fvi
> A OmicABELnoMM/examples/interactions/INT01R.fvi
> A OmicABELnoMM/examples/interactions/XL.fvd
> A OmicABELnoMM/examples/interactions/INT1RR.fvi
> A OmicABELnoMM/examples/interactions/XL.fvi
> A OmicABELnoMM/examples/interactions/XR.fvd
> A OmicABELnoMM/examples/interactions/INT10.fvd
> A OmicABELnoMM/examples/interactions/INT01.fvd
> A OmicABELnoMM/examples/interactions/INT11.fvd
> A OmicABELnoMM/examples/interactions/INTR0.fvd
> A OmicABELnoMM/examples/interactions/INTR1.fvd
> A OmicABELnoMM/examples/interactions/INTRR.fvd
> A OmicABELnoMM/examples/interactions/XR.fvi
> A OmicABELnoMM/examples/interactions/INT10.fvi
> A OmicABELnoMM/examples/interactions/INT01.fvi
> A OmicABELnoMM/examples/dosages_1.txt
> A OmicABELnoMM/examples/dosages_2.txt
> A OmicABELnoMM/examples/XL.fvi
> A OmicABELnoMM/examples/Y.fvd
> A OmicABELnoMM/examples/XR.fvd
> A OmicABELnoMM/examples/Y.fvi
> A OmicABELnoMM/examples/XR.fvi
> A OmicABELnoMM/examples/CreateData.R
> U OmicABELnoMM
> Checked out revision 1849.
> ╭─lennart at barabas /tmp
> ╰─$ cd OmicABELnoMM
> ╭─lennart at barabas /tmp/OmicABELnoMM
> ╰─$ autoreconf -fi
> configure.ac:6: installing './install-sh'
> configure.ac:6: installing './missing'
> Makefile.am: installing './depcomp'
> ╭─lennart at barabas /tmp/OmicABELnoMM
> ╰─$
>
>
>> From here I can install the MPI script I suppose.
>
> Indeed.
>
>>
>> I will commit what I got so far from the documentation, because My
>> instructions to install are all wrong now since users wont use svn to
>> download and compile the code. Feel free to add your own installation
>> procedure and modify the tex file.
>
> Sure, I'll do that. It will mostly be a copy/paste from the ProbABEL manual.
>
>
> Lennart.
>
>
>
>>
>> -Alvaro
>>
>> ________________________________________
>> From: genabel-devel-bounces at lists.r-forge.r-project.org [genabel-devel-bounces at lists.r-forge.r-project.org] on behalf of Frank, Alvaro Jesus [alvaro.frank at rwth-aachen.de]
>> Sent: Monday, October 27, 2014 12:49 PM
>> To: L.C. Karssen; genabel-devel at lists.r-forge.r-project.org
>> Subject: Re: [GenABEL-dev] LATEX error on autoreconf
>>
>> On a different NON 32bit system:
>> alvaro.frank@:/opt/omicabelnomm> svn checkout svn://svn.r-forge.r-project.org/svnroot/genabel/pkg/OmicABELnoMM/
>> A OmicABELnoMM/OmicOUT
>> A OmicABELnoMM/OmicOUT/main.cpp
>> A OmicABELnoMM/AUTHORS
>> A OmicABELnoMM/ChangeLog
>> A OmicABELnoMM/src
>> A OmicABELnoMM/src/AIOwrapper.h
>> A OmicABELnoMM/src/Definitions.h
>> A OmicABELnoMM/src/Utility.cpp
>> A OmicABELnoMM/src/main.cpp
>> A OmicABELnoMM/src/Algorithm.cpp
>> A OmicABELnoMM/src/Utility.h
>> A OmicABELnoMM/src/AIOwrapper.cpp
>> A OmicABELnoMM/src/Algorithm.h
>> A OmicABELnoMM/compile
>> A OmicABELnoMM/libs
>> A OmicABELnoMM/libs/include
>> A OmicABELnoMM/libs/lib
>> A OmicABELnoMM/README
>> A OmicABELnoMM/tests
>> A OmicABELnoMM/tests/test.cpp
>> A OmicABELnoMM/tests/Makefile.am
>> A OmicABELnoMM/configure.ac
>> A OmicABELnoMM/doc
>> A OmicABELnoMM/doc/howtocompile.txt
>> A OmicABELnoMM/doc/UserGuide.tex
>> A OmicABELnoMM/INSTALL
>> A OmicABELnoMM/COPYING
>> A OmicABELnoMM/test-driver
>> A OmicABELnoMM/Makefile.am
>> A OmicABELnoMM/NEWS
>> A OmicABELnoMM/examples
>> A OmicABELnoMM/examples/XL.fvd
>> A OmicABELnoMM/examples/results
>> A OmicABELnoMM/examples/exclude_individuals.txt
>> A OmicABELnoMM/examples/interactions
>> A OmicABELnoMM/examples/interactions/INTR0.fvi
>> A OmicABELnoMM/examples/interactions/INT11.fvi
>> A OmicABELnoMM/examples/interactions/INTR1.fvi
>> A OmicABELnoMM/examples/interactions/INTRR.fvi
>> A OmicABELnoMM/examples/interactions/Y.fvd
>> A OmicABELnoMM/examples/interactions/INT0.fvd
>> A OmicABELnoMM/examples/interactions/INT1.fvd
>> A OmicABELnoMM/examples/interactions/INTR.fvd
>> A OmicABELnoMM/examples/interactions/INT011.fvd
>> A OmicABELnoMM/examples/interactions/Y.fvi
>> A OmicABELnoMM/examples/interactions/INT01R.fvd
>> A OmicABELnoMM/examples/interactions/INT0.fvi
>> A OmicABELnoMM/examples/interactions/INT1RR.fvd
>> A OmicABELnoMM/examples/interactions/INT1.fvi
>> A OmicABELnoMM/examples/interactions/INTR.fvi
>> A OmicABELnoMM/examples/interactions/INT011.fvi
>> A OmicABELnoMM/examples/interactions/INT01R.fvi
>> A OmicABELnoMM/examples/interactions/XL.fvd
>> A OmicABELnoMM/examples/interactions/INT1RR.fvi
>> A OmicABELnoMM/examples/interactions/XL.fvi
>> A OmicABELnoMM/examples/interactions/XR.fvd
>> A OmicABELnoMM/examples/interactions/INT10.fvd
>> A OmicABELnoMM/examples/interactions/INT01.fvd
>> A OmicABELnoMM/examples/interactions/INT11.fvd
>> A OmicABELnoMM/examples/interactions/INTR0.fvd
>> A OmicABELnoMM/examples/interactions/INTR1.fvd
>> A OmicABELnoMM/examples/interactions/INTRR.fvd
>> A OmicABELnoMM/examples/interactions/XR.fvi
>> A OmicABELnoMM/examples/interactions/INT10.fvi
>> A OmicABELnoMM/examples/interactions/INT01.fvi
>> A OmicABELnoMM/examples/dosages_1.txt
>> A OmicABELnoMM/examples/dosages_2.txt
>> A OmicABELnoMM/examples/XL.fvi
>> A OmicABELnoMM/examples/Y.fvd
>> A OmicABELnoMM/examples/XR.fvd
>> A OmicABELnoMM/examples/Y.fvi
>> A OmicABELnoMM/examples/XR.fvi
>> A OmicABELnoMM/examples/CreateData.R
>> U OmicABELnoMM
>> Checked out revision 1849.
>> alvaro.frank at rhein:/opt/omicabelnomm> cd OmicABELnoMM/
>> alvaro.frank at rhein:/opt/omicabelnomm/OmicABELnoMM> autoreconf -fi
>> configure.ac:53: error: possibly undefined macro: AC_MSG_FAILURE
>> If this token and others are legitimate, please use m4_pattern_allow.
>> See the Autoconf documentation.
>> configure.ac:55: error: possibly undefined macro: AC_MSG_NOTICE
>> autoreconf: /usr/bin/autoconf failed with exit status: 1
>> alvaro.frank@:/opt/omicabelnomm/OmicABELnoMM> lscpu
>> Architecture: x86_64
>> CPU op-mode(s): 32-bit, 64-bit
>> Byte Order: Little Endian
>> CPU(s): 48
>> On-line CPU(s) list: 0-47
>> Thread(s) per core: 1
>> Core(s) per socket: 12
>> CPU socket(s): 4
>> NUMA node(s): 8
>> Vendor ID: AuthenticAMD
>> CPU family: 16
>> Model: 9
>> Stepping: 1
>> CPU MHz: 800.000
>> BogoMIPS: 4200.05
>> Virtualization: AMD-V
>> L1d cache: 64K
>> L1i cache: 64K
>> L2 cache: 512K
>> L3 cache: 5118K
>> NUMA node0 CPU(s): 0-5
>> NUMA node1 CPU(s): 6-11
>> NUMA node2 CPU(s): 12-17
>> NUMA node3 CPU(s): 18-23
>> NUMA node4 CPU(s): 24-29
>> NUMA node5 CPU(s): 30-35
>> NUMA node6 CPU(s): 36-41
>> NUMA node7 CPU(s): 42-47
>> alvaro.frank@:/opt/omicabelnomm/OmicABELnoMM>
>>
>> ________________________________________
>> From: genabel-devel-bounces at lists.r-forge.r-project.org [genabel-devel-bounces at lists.r-forge.r-project.org] on behalf of Frank, Alvaro Jesus [alvaro.frank at rwth-aachen.de]
>> Sent: Monday, October 27, 2014 12:41 PM
>> To: L.C. Karssen; genabel-devel at lists.r-forge.r-project.org
>> Subject: Re: [GenABEL-dev] LATEX error on autoreconf
>>
>> I think the 32bit problem is the fault here.
>> 32 bit architecture is a valid working environment for most, i.e: Here at helmoholtz.
>>
>>
>>
>> ________________________________________
>> From: genabel-devel-bounces at lists.r-forge.r-project.org [genabel-devel-bounces at lists.r-forge.r-project.org] on behalf of L.C. Karssen [lennart at karssen.org]
>> Sent: Monday, October 27, 2014 12:40 PM
>> To: genabel-devel at lists.r-forge.r-project.org
>> Subject: Re: [GenABEL-dev] LATEX error on autoreconf
>>
>> When googling:
>>
>> On 27-10-14 12:34, L.C. Karssen wrote:
>>> possibly undefined macro: AC_MSG_FAILURE
>>>> If this token and others are legitimate, please use m4_pattern_allow.
>>
>> I got a link to a StackOverflow post [1] that says that you may not have
>> pkg-config installed. However, I think that pkg-config is installed by
>> default (because when trying to remove it I get lots of package
>> dependencies). An other suggestion in that SO question is that it may be
>> related to 32 bits architecture...
>>
>>
>> Lennart.
>>
>>
>> [1]
>> http://stackoverflow.com/questions/8811381/possibly-undefined-macro-ac-msg-error
>>
>> --
>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
>> L.C. Karssen
>> Utrecht
>> The Netherlands
>>
>> lennart at karssen.org
>> http://blog.karssen.org
>> GPG key ID: A88F554A
>> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>>
>> _______________________________________________
>> genabel-devel mailing list
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>> _______________________________________________
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>>
>
> --
> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
> L.C. Karssen
> Utrecht
> The Netherlands
>
> lennart at karssen.org
> http://blog.karssen.org
> GPG key ID: A88F554A
> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>
--
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
L.C. Karssen
Utrecht
The Netherlands
lennart at karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
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