Compiling Issue for nvExtractReads

[Brad Pfeffer]

Hi, I'm running a server with Centos 6.5(64-bit) and gcc 4.8.2 and I am having an issue where everything else seems to compile, but I get some errors for nvExtractReads:

 

/data/nvbio-master/nvExtractReads.cu(236): error: "ASCII" is ambiguous

/data/nvbio-master/nvExtractReads.cu(259): error: "ASCII" is ambiguous

/data/nvbio-master/nvExtractReads.cu(296): error: "ASCII" is ambiguous

/data/nvbio-master/nvExtractReads.cu(333): error: "ASCII" is ambiguous

 

4 errors detected in the comilation of  "tmp/tmpxft_00009596_00000000-6_nvExtractReads.cpp1.ii".

CMake Error at nvExtractReads_generated_nvExtractReads.cu.o.cmake:264 (message):

Error generating file

/data/nvbio-master/build/nvExtractReads/CMakeFiles/nvExtractReads.dir//./nvExtractReads_generated_nvExtractReads.cu.o

 

 

I'm a bit unsure of what the problem is, I investigated a bit but I only found things that didn't quite lead anywhere, like enum need to use integers(instead of the 0u) unless you're using c++11. Any help would be greatly appreciated!

 

Thanks,

Brad

[Nuno Subtil]

Hi Brad,

We don’t have a CentOS system to test this on right now. I can’t reproduce the same error you’re getting on my environment, but admittedly mine is quite different.

Based on your email, this looks very much like it could be a compiler issue. Is there any chance you can test with a newer compiler? Either gcc 4.9.x or even just a later revision from the 4.8.x series might be enough. If that’s not possible or easy to do for you, we can try to replicate this on our end. It might take a little longer for us to get set up for this, so I thought I’d offer this as a quick experiment.

You could also try replacing the offending ASCII constants with Format::ASCII to see if that makes your compiler happier — we’d be happy to take a patch for this if it works for you!

Nuno

--
You received this message because you are subscribed to the Google Groups "nvbio-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to nvbio-users...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

---

This email message is for the sole use of the intended recipient(s) and may contain confidential information.  Any unauthorized review, use, disclosure or distribution is prohibited.  If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message.

---

[Brad Pfeffer]

Unfortunately, trying to push CentOS too far on certain things ends up being a huge hassle, it was enough work upgrading gcc from 4.4.7 to 4.8.2 via their devtoolset. As for the switching of the ASCII, I'm not very confident in my C++ and not sure the proper way to handle this. I thought ASCII was just being used as a value in an enum to be referenced, If you could give me a quick guide to the before and after(or, a quick patch as you said) I could try that.

 

I'd hate for you to go to a lot of trouble if no one else has this problem, how integral is nvExtractReads to the entirety of nvbio and can it work without it? I couldn't find much documentation on some of the parts that weren't nvBowtie, though our local tests with nvBowtie do look promising compared to throwing a boatload of cpu cores at alignments.