compiling with google sparsehash 1.8.1

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Arthur Pastuer

Aug 3, 2010, 4:45:56 PM8/3/10
to ABySS

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?


Rod Docking

Aug 3, 2010, 4:50:10 PM8/3/10
to Arthur Pastuer, ABySS
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/


Mar 26, 2018, 7:03:04 PM3/26/18
to ABySS

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

Mar 27, 2018, 11:15:27 AM3/27/18
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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Mar 29, 2018, 4:44:52 PM3/29/18
to ABySS
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?



Ben Vandervalk

Mar 29, 2018, 6:05:44 PM3/29/18
I've seen this error before... try connecting `--with-sparsehash` and the path with an equals sign, e.g:


- Ben
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