#1630 rdkit build fails with cmake error

[John Bollinger]

Attempts to build rdkit-2013.03.02-1 under a fully up-to-date (as of 2013-July-19) fink 0.35.1 reliably fail with an error from cmake, the crux of which is:

---

CMake Error at /sw/share/cmake-2.8/Modules/Platform/Darwin.cmake:190 (message):
CMAKE_OSX_DEPLOYMENT_TARGET is '10.8' but CMAKE_OSX_SYSROOT:

""

is not set to a MacOSX SDK with a recognized version. Either set
CMAKE_OSX_SYSROOT to a valid SDK or set CMAKE_OSX_DEPLOYMENT_TARGET to
empty.
Call Stack (most recent call first):
/sw/share/cmake-2.8/Modules/CMakeSystemSpecificInformation.cmake:36 (include)
CMakeLists.txt:6 (project)

---

Based on reports of similar problems for other packages, it looks like this issue results from a change in cmake behavior first appearing in cmake 2.8.10. See, for example, this discussion: http://www.mail-archive.com/fink-users@lists.sourceforge.net/msg37643.html.

The "universal" solution reported in that e-mail thread (an update to kde4-buildenv) does not seem to solve the issue for rdkit, but some of the e-mails describe how a package-specific solution might be implemented. On the other hand, this issue likely affects other packages as well, so if a truly universal solution can be devised then that would be better.

[Hanspeter Niederstrasser]

Assigning to rdkit maintainer.

I do not see this on 10.7.

[John Bollinger]

I observed the issue on 10.8, with Xcode 4.5.

Some similar reports I saw while researching the issue suggested that although it is specific to the latest cmake, it is not tied to a particular version of OS X. I did not carefully investigate the version dependencies, however.

[William Scott]

I cannot reproduce it either. I'm on Xcode 4.6, otherwise all is the same, and I have previously built it with Xcode 4.5.

I also couldn't get John's sourceforge email to work; it bounces the reply.

[William Scott]

Have you issued the command

sudo xcodebuild -license

recently? I find occasionally that cryptic errors are the result of not doing this.

[atlauren]

May be related/identical to:
https://sourceforge.net/p/fink/package-submissions/4297/

As noted herein, I've had problems with packages that rely on cmake if installing with command tools only. The problem "goes away" if the complete XCode is installed.

[William Scott]

OK, I managed to reproduce it and I think solve the problem.

Add cmake arguments:

cmake -DCMAKE_OSX_SYSROOT:PATH="/" -DCMAKE_OSX_DEPLOYMENT_TARGET:STRING=""

[John Bollinger]

I do have the complete Xcode installed, so I don't think this issue is the same as issue 4297.

Anyway, rdkit now builds cleanly for me with the change Bill made. At least I assume he made it -- it appears in the rdkit finkinfo on the stable branch as of at least yesterday, but I'm now testing on a different, fresh, system (also OSX 10.8 / XCode 4.5).

However, building coot based on the result fails with a slew of errors involving files rdkit-interface.cc, use-rdkit.hh, and rdkit-interface.hh. It looks like about 20 header files are not found, most of them under RDGeneral/ or GraphMol/, including GraphMol/RDKitBase.h. I am supposing that the missing headers are supposed to be part of rdkit, but I don't find any header files at all in any of the three built rdkit DEBs.

[Hanspeter Niederstrasser]

[Hanspeter Niederstrasser]

Multiple updates to coot have happened since your report in July. Do you still see the error?

[John Bollinger]

No, Coot now builds fine for me. In addition to an update to coot, an update to rdkit was also required, but it all seems sorted out now.

[Hanspeter Niederstrasser]

Thanks for confirming. Closing.