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jts / sga

de novo sequence assembler using string graphs
http://genome.cshlp.org/content/22/3/549
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configure not working #114

Closed Sameth closed 8 years ago

Sameth commented 8 years ago

Running ./configure with appropriate paths to bamtools and sparsehash yields the following:

checking google/sparse_hash_set usability... no checking google/sparse_hash_set presence... yes configure: WARNING: google/sparse_hash_set: present but cannot be compiled configure: WARNING: google/sparse_hash_set: check for missing prerequisite headers? configure: WARNING: google/sparse_hash_set: see the Autoconf documentation configure: WARNING: google/sparse_hash_set: section "Present But Cannot Be Compiled" configure: WARNING: google/sparse_hash_set: proceeding with the compiler's result configure: WARNING: ## -------------------------------- ## configure: WARNING: ## Report this to js18@sanger.ac.uk ## configure: WARNING: ## -------------------------------- ## checking for google/sparse_hash_set... no configure: error: google sparse hash library is required: http://code.google.com/p/google-sparsehash/

jts commented 8 years ago

Hi,

Can you let me know what version of sparsehash you used, and the version of gcc?

Thanks, Jared

On Apr 23, 2016, at 10:09 AM, Jaroslav Petrucha notifications@github.com wrote:

Running ./configure with appropriate paths to bamtools and sparsehash yields the following:

checking google/sparse_hash_set usability... no checking google/sparse_hash_set presence... yes configure: WARNING: google/sparse_hash_set: present but cannot be compiled configure: WARNING: google/sparse_hash_set: check for missing prerequisite headers? configure: WARNING: google/sparse_hash_set: see the Autoconf documentation configure: WARNING: google/sparse_hash_set: section "Present But Cannot Be Compiled" configure: WARNING: google/sparse_hash_set: proceeding with the compiler's result configure: WARNING: ## -------------------------------- ## configure: WARNING: ## Report this to js18@sanger.ac.uk ## configure: WARNING: ## -------------------------------- ## checking for google/sparse_hash_set... no configure: error: google sparse hash library is required: http://code.google.com/p/google-sparsehash/

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Sameth commented 8 years ago

Hello,

I've already found a work-around, but first things first.

Gcc version: 4.9.2 (Ubuntu 4.9.2-10ubuntu13) Sparsehash: used the last version from repo (i. e. this commit: https://github.com/sparsehash/sparsehash/commit/4a36398d442cc86f47d2d7e751596cc2430ad135 ).

I have -std=c++11 in my CXXFLAGS, but even changing that to c++03 didn't help. What did help was reinstalling sparsehash with c++03 (duh).

Thanks for your interest, Jaroslav Petrucha

jts commented 8 years ago

Thanks for reporting back, sorry it took me so long to reply. It sounds like this issue is resolved so I'll close it.

weijianwen commented 7 years ago

Similar errors arise when building SGA with GCC 6. Rebuiling SGA with GCC 5.4 and sparsehash 2.0.3 (without modifying flags) solves this issues.

odoublewen commented 5 years ago

I would love to figure out how to get sga to compile with modern versions of gcc.

I have a tree of tools that I compile with gcc 8.2.0 , but I run into the same issue reported here. I'll try to figure it out and report back anything I learn.... if anyone else has suggestions, I'd also appreciate them!

numpde commented 4 years ago

Same problem with gcc (Ubuntu 9.3.0-10ubuntu2) 9.3.0

sparsehash 2.0.3-1 installed with sudo apt install libsparsehash-dev

Rohit-Satyam commented 3 years ago

Did anyone got success in resolving this problem??