Building trunk in current Mac OS X

Development
1

Hi all.

Since the recent introduction of “cmake/modules/MacroEnsureVersion.cmake:95 (NORMALIZE_VERSION)”

I get this:

"cmake -DCMAKE_C_FLAGS=-m32 -DCMAKE_CXX_FLAGS=-m32 -DOPENBABEL2_INCLUDE_DIR=/usr/local/include/openbabel-2.0 -D-DOPENBABEL2_LIBRARIES=/usr/local/lib/libopenbabel.dylib -DOPENBABEL2_VERSION_MET=true -DENABLE_PYTHON=NO …
– The C compiler identification is GNU
– The CXX compiler identification is GNU
– Check for working C compiler: /usr/bin/gcc
– Check for working C compiler: /usr/bin/gcc – works
– Detecting C compiler ABI info
– Detecting C compiler ABI info - done
– Check for working CXX compiler: /usr/bin/c++
– Check for working CXX compiler: /usr/bin/c++ – works
– Detecting CXX compiler ABI info
– Detecting CXX compiler ABI info - done
– The build type is RelWithDebInfo
– Performing Test HAVE_GCC_VISIBILITY
– Performing Test HAVE_GCC_VISIBILITY - Success
– Performing Test COMPILES_WITHOUT_FPERMISSIVE
– Performing Test COMPILES_WITHOUT_FPERMISSIVE - Success
– Looking for Q_WS_X11
– Looking for Q_WS_X11 - not found.
– Looking for Q_WS_WIN
– Looking for Q_WS_WIN - not found.
– Looking for Q_WS_QWS
– Looking for Q_WS_QWS - not found.
– Looking for Q_WS_MAC
– Looking for Q_WS_MAC - found
– Looking for QT_MAC_USE_COCOA
– Looking for QT_MAC_USE_COCOA - not found.
– Found Qt-Version 4.5.3
– Found OpenSSL: /usr/lib/libssl.dylib
– Found lupdate: /usr/bin/lupdate
– Found lrelease: /usr/bin/lrelease
– Found lconvert: /usr/bin/lconvert
– Found Eigen2: /usr/local/include/eigen2
– Found ZLIB: /usr/lib/libz.dylib
– Found OpenBabel 2.2 or later: /usr/local/lib/libopenbabel.dylib
– Found OpenBabel2 executable: /usr/local/bin/babel
CMake Error at cmake/modules/MacroEnsureVersion.cmake:95 (NORMALIZE_VERSION):
NORMALIZE_VERSION Macro invoked with incorrect arguments for macro named:
NORMALIZE_VERSION
Call Stack (most recent call first):
cmake/modules/FindOpenBabel2.cmake:108 (macro_ensure_version)
CMakeLists.txt:130 (find_package)

– Git revision found to be 953039a
– Found Git revision is: 953039a
– Building development version from Git clone.
– Python support disabled.
– Threaded OpenGL rendering not enabled
– RPath support enabled for installed binaries and libraries
– docbook tools not found, doc targets disabled
– Configuring incomplete, errors occurred!"

Since “FindOpenBabel2.cmake” does not work on a Mac,
I am stuck. Issuing a simple “cmake …” in build generates errors.
Same thing with cmake 2.8 and similar build request under linux:
"cmake -DCMAKE_C_FLAGS=-m32 -DCMAKE_CXX_FLAGS=-m32 -DOPENBABEL2_INCLUDE_DIR=/usr/local/include/openbabel-2.0 -D-DOPENBABEL2_LIBRARIES=/usr/local/lib/libopenbabel.dylib -DOPENBABEL2_VERSION_MET=true …"
yields cmake errors.

Any sugestions welcome,

Cheers,

Louis

2

Louis Ricard wrote:

Hi all.

Since the recent introduction of “cmake/modules/MacroEnsureVersion.cmake:95 (NORMALIZE_VERSION)”

I am working on getting the Avogadro dashboard up and running again.
Kitware has generously given Avogadro and Open Babel silver CDash
accounts, this means that we can have unlimited users and builds. In
CMake 2.8.0 native support for Git was also added. I will be cronning a
couple of Linux build hosts,

I am hoping that Geoff can take care of some Mac build hosts. If you
have a system you are able to leave on overnight I could help you get a
CDash client set up so that you can submit build tests from the latest
Avogadro and Open Babel. This is the best way to ensure that Avogadro
and Open Babel continue to function on the big three OSes at least.

See http://my.cdash.org/ for details - the Avogadro project is up on
there. I have some new scripts, although currently I am not in a
position to run a Windows submission host. I could help anyone who might
be able to do that though.

I will try to take a look at the new CMake code in the morning.

Marcus

3

Hi.

Oddly, I can’t build a working OB in Mac OS X 10.6.2 using cmake (2.6p4 or 2.80).
Running something like “babel xxx.res xxx.pdb”, I always get this kind of error :
“macbook-de-louis-ricard:audrey ricard$ babel pa142.res pa142.xyz
babel: cannot write output format!
Open Babel 2.2.99 – Dec 5 2009 – 20:30:14
Usage: babel [-i] [-o]
Try -H option for more information.”

And the “babel -H” command yields:

"Open Babel converts chemical structures from one file format to another

Usage: babel [Options]

Each spec can be a file whose extension decides the format.
Optionally the format can be specified by preceding the file by
-i e.g. -icml, for input and -o for output

See below for available format-types, which are the same as the
file extensions and are case independent.
If no input or output file is given stdin or stdout are used instead.

More than one input file can be specified and their names can contain
wildcard chars (* and ?).The molecules are aggregated in the output file.

Conversion options
-f <#> Start import at molecule # specified
-l <#> End import at molecule # specified
-e Continue with next object after error, if possible
-z Compress the output with gzip
-k Attempt to translate keywords
-H Outputs this help text
-Hxxx (xxx is file format ID e.g. -Hcml) gives format info
-Hall Outputs details of all formats
-V Outputs version number
-L Lists plugin classes of this type
e.g. , or for a list of BaseTypes
-m Produces multiple output files, to allow:
Splitting: e.g. babel infile.mol new.smi -m
puts each molecule into new1.smi new2.smi etc
Batch conversion: e.g. babel *.mol -osmi -m
converts each input file to a .smi file
The following file formats are recognized:
formats is not a recognized plugin type. Those with instances of sub-types loaded are:
descriptors
fingerprints
forcefields
loaders
ops

See further specific info and options using -H, e.g. -Hcml"

I am quite puzzled.

Unfortunately, I do not have a system a can leave running
overnight at the moment. Sorry.

Cheers,

Louis

Le 5 déc. 2009 à 02:04, Marcus D. Hanwell a écrit :

Louis Ricard wrote:

Hi all.

Since the recent introduction of “cmake/modules/MacroEnsureVersion.cmake:95 (NORMALIZE_VERSION)”

I am working on getting the Avogadro dashboard up and running again.
Kitware has generously given Avogadro and Open Babel silver CDash
accounts, this means that we can have unlimited users and builds. In
CMake 2.8.0 native support for Git was also added. I will be cronning a
couple of Linux build hosts,

I am hoping that Geoff can take care of some Mac build hosts. If you
have a system you are able to leave on overnight I could help you get a
CDash client set up so that you can submit build tests from the latest
Avogadro and Open Babel. This is the best way to ensure that Avogadro
and Open Babel continue to function on the big three OSes at least.

See http://my.cdash.org/ for details - the Avogadro project is up on
there. I have some new scripts, although currently I am not in a
position to run a Windows submission host. I could help anyone who might
be able to do that though.

I will try to take a look at the new CMake code in the morning.

Marcus

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