[GenABEL-dev] LATEX error on autoreconf

Frank, Alvaro Jesus alvaro.frank at rwth-aachen.de
Mon Oct 27 13:24:30 CET 2014 

How do I add the MPI .m4 file to autoconf without modifying the configure.ac?

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
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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
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