Re: [Sra-tools] Dynamic linking of sra-toolkit version 2.1.3 and above.

[SRA Toolkit Development Group <sra-tools@ncbi.nlm.nih.gov>]

We did make a change of default target from 
"release" to "pubtools", where the latter is 
forcefully static.

If you have already performed a build, you may 
want to "make clean" before anything else.

The steps to put things back to normal would be:

$ make release dynamic

and then things should be as you were expecting. 
"make release" will create symlinks within 
$OUTDIR to binaries and libraries.

You are going to need to move up much closer to 
the current release now that we are building cSRA 
objects within NCBI's archive. We expect to 
release 2.1.9 early this week. Older code bases 
will not be able to manage the schemas found 
within new object types.

Thanks, and let us know how it goes.

SRA Toolkit Team


At 9:13 AM -0500 1/9/12, Charles Plessy wrote:
> Le Mon, Jan 09, 2012 at 07:49:09AM -0500, SRA 
> Toolkit Development Group a écrit :
> >  Can you be more specific? There was no intentional loss of dynamic
> >  linking, and we still build our system dynamically.
>
> The following commands give me different results on 2.1.2 and 2.1.3.
>
>   make dynamic
>   export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$OUTDIR/lib64"
>   make
>
> In 2.1.2 and earlier, the resulting compiler options are typically:
>
>   -c  -DNDEBUG  -m64    -D_LOGGING 
> -D_ARCH_BITS=64 -DLINUX -DUNIX -D_GNU_SOURCE
>   -D_REENTRANT -D_FILE_OFFSET_BITS=64 -I/tmp/sra_sdk-2.1.2/libs/klib/linux
>   -I/tmp/sra_sdk-2.1.2/libs/klib/unix -I/tmp/sra_sdk-2.1.2/libs/klib
>   -I/tmp/sra_sdk-2.1.2/interfaces 
> -I/tmp/sra_sdk-2.1.2/interfaces/cc/gcc/x86_64
>   -I/tmp/sra_sdk-2.1.2/interfaces/cc/gcc 
> -I/tmp/sra_sdk-2.1.2/interfaces/os/linux
>   -I/tmp/sra_sdk-2.1.2/interfaces/os/unix 
> -I/tmp/sra_sdk-2.1.2/interfaces/ext -MD
>   -fPIC -O3 -fno-strict-aliasing -D_LIBRARY
>
> While in 2.1.3 and later they are:
>
>   -c  -DNDEBUG  -m64   -D_STATIC -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT
>   -D_FILE_OFFSET_BITS=64 -D_ARCH_BITS=64 -DLIBPREFIX=lib -DSHLIBEXT=so
>   -I/tmp/sra_sdk-2.1.3/libs/klib/linux -I/tmp/sra_sdk-2.1.3/libs/klib/unix
>   -I/tmp/sra_sdk-2.1.3/libs/klib -I/tmp/sra_sdk-2.1.3/interfaces
>   -I/tmp/sra_sdk-2.1.3/interfaces/cc/gcc/x86_64
>   -I/tmp/sra_sdk-2.1.3/interfaces/cc/gcc 
> -I/tmp/sra_sdk-2.1.3/interfaces/os/linux
>   -I/tmp/sra_sdk-2.1.3/interfaces/os/unix 
> -I/tmp/sra_sdk-2.1.3/interfaces/ext -MD
>   -fPIC -O3 -fno-strict-aliasing -D_LIBRARY
>
> Accordingly, the build in 2.1.3 is static, as 
> witnessed by the absence of files
> in <OUTDIR>/mod64/.
>
> Best,
>
> --
> Charles
>
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