[GenABEL-dev] LATEX error on autoreconf

Frank, Alvaro Jesus alvaro.frank at rwth-aachen.de
Mon Oct 27 13:03:47 CET 2014 

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",' 

>From here I can install the MPI script I suppose.

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.

-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

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L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org
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