compiling with google sparsehash 1.8.1

[Arthur Pastuer]

Hi,

I am installing ABySS on a remote computer where I do not have root
privileges. Sparsehash is therefore installed in my home directory and
not its default location. Because of this I am having trouble
compiling using sparsehash. I believe that I just need to tell ABySS
or ./configure where to look for sparsehash. How can this be done?

Best,
Art

[Rod Docking]

Hi Art,

From the ABySS README file:

ABySS should be built using Google sparsehash to reduce memory usage,

although it will build without. Google sparsehash should be found in

/usr/include or its location specified to configure:

./configure CPPFLAGS=-I/usr/local/include

I do something like:

./configure CPPFLAGS=-I/home/rdocking/sandbox/sparsehash/include/

Cheers,

Rod

Rod Docking

rdoc...@bcgsc.ca

(604) 707-5900 ext. 675407

[megank...@gmail.com]

Hi,

I have the same problem. When I specify the location of spasehash using CPPFLAGS=/path/include/

I get 

configure: error: C compiler cannot create executables

How can I get the correct location of sparsehash?

[Ben Vandervalk]

Hi there,

I think you are missing the "-I" in front of "/path/include" (compare to Rod's example below).  You can look inside `config.log` to get more information about your error, although it is difficult to understand unless you are a C/C++ programmer.

`configure` also has a `--with-sparsehash` option.  (To get a list of available options, type `./configure --help`.)  In the case of `--with-sparsehash`, you need to give it the *parent* directory of the `include` directory, i.e.  `/path` instead of `/path/include`.

- Ben

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[megank...@gmail.com]

Hi Ben,

Thanks for your help. I have tried including the "-l" but I think there is still something wrong with the way I have configured sparsehash maybe?

I had better luck using the "-with--sparsehash" option, but it fails at this step of configure:

checking build system type... Invalid configuration `//mnt/data/kevin/rnaseq/tools/include/': machine `//mnt/data/kevin/rnaseq/tools/include/' not recognized

What does this mean?

Thanks,

Megan

[Ben Vandervalk]

I've seen this error before... try connecting `--with-sparsehash` and the path with an equals sign, e.g:

--with-sparsehash=/mnt/data/kevin/rnaseq/tools

- Ben