Compilation problems on Linux

[statgen]

Compilation problems on Linux

[mktrost]

Do you know where in the code CXXFLAGS is used? I think it is only using CFLAGS. But maybe it should be switching for C++ vs C.

But I am noticing that there would be a compile problem if CFLAGS is already defined in the user's environment.
The Makefiles only set CFLAGS with the appropriate settings (most of which you discovered and fixed on your own) if it is not already set. Is that the case for you? Do you have CFLAGS already set in your environment?

Thanks for pointing this out.
I will try to rework the logic so it ensures the required settings are used even if CFLAGS is already set.

I'm sorry you ran into so many compile issues. Thank you for taking the time to update us on what you found/fixed.

[vinjana]

The Makefiles only set CFLAGS with the appropriate settings (most of which you discovered and fixed on your own) if it is not already set. Is that the case for you? Do you have CFLAGS already set in your environment?

Yes.

Do you know where in the code CXXFLAGS is used? I think it is only using CFLAGS. But maybe it should be switching for C++ vs C.

Yes. I usually keep CXXFLAGS and CFLAGS in sync.

[sjackman]

I see this compiler error with version 1.0.7, but not on the HEAD. I'm glad to see that this bug is fixed on HEAD. Could you please release a new stable version of bamUtils where this bug is fixed?

g++  -Os -w -pipe -march=core2 -msse4 -o obj/SamFileHeader.o -c SamFileHeader.cpp -DVERSION="\"1.0.0\""
In file included from SamFileHeader.h:24:0,
                 from SamFileHeader.cpp:18:
SamReferenceInfo.h:21:25: fatal error: StringArray.h: No such file or directory
compilation terminated.
make[2]: *** [obj/SamFileHeader.o] Error 1

Thanks,
Shaun

[sjackman]

An update to my previous comment. The git tag 1.0.7 builds fine, but the tarball 1.0.7 gives the above error.

[mktrost]

When you used the one from git, what version of the library did you use?
The latest?
Unfortunately I'm out on vacation and don't have access to release a new
version. I will release a new version when I get back in June. Thank you
for your patience, and I am glad you found a work around.

Mary Kate Wing

On Tue, May 21, 2013 at 6:33 PM, Shaun Jackman [email protected]:

An update to my previous comment. The git tag 1.0.7https://github.com/statgen/bamUtil/archive/v1.0.7.tar.gzbuilds fine, but the tarball
1.0.7http://genome.sph.umich.edu/w/images/5/5d/BamUtilLibStatGen.1.0.7.tgzgives the above error.

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/4#issuecomment-18246261
.

[sjackman]

Yes, I used the latest library. It can certainly wait until you get back. Enjoy your vacation, Mary.

[mktrost]

Sorry for the delay. I have release version 1.0.9. Hopefully that version has these problems fixed as it is the latest version.

[sjackman]

Works for me. Thanks, Mary.