Re: Attempt to upgrade sra-sdk

Hi Aaron,

Am Sat, Dec 09, 2023 at 08:23:26PM -0500 schrieb Aaron M. Ucko:
> 
> AFAICT, the immediate problem is that label_online_tests.patch refers to
> at least one removed or renamed test:
> 
>   CMake Error at test/internal/vdb-diff/CMakeLists.txt:42 (set_tests_properties):
>     set_tests_properties Can not find test to add properties to:
>       Test_VDB_Diff_Check_success
> 
> Temporarily disabling this patch will let you focus on compilation
> issues for the time being.

We'll probably leave this for later
 
> Please also bear in mind that upstream maintains this code in
> conjunction with ncbi-vdb (lower-level) and ngs-sdk (higher-level), so
> it may help to update ncbi-vdb first and you may want to update ngs-sdk
> afterwards.

I should have known this but unfortunately I forgot.  I've pushed the
latest version of ncbi-vdb with patches adapted but get:

No mbedtls libs found installed in the system, using local copy...
-- Configuring done (1.1s)
CMake Error at libs/ncbi-vdb/CMakeLists.posix.txt:56 (add_library):
  Error evaluating generator expression:
  
    $<TARGET_OBJECTS:mbedx509>
  
  Objects of target "mbedx509" referenced but no such target exists.
Call Stack (most recent call first):
  libs/ncbi-vdb/CMakeLists.txt:84 (include)

  
CMake Error at build/common.cmake:185 (add_library):
  Error evaluating generator expression:

    $<TARGET_OBJECTS:mbedx509>

  Objects of target "mbedx509" referenced but no such target exists.


which is strange since libmbedtls-dev is in Build-Depends.  I'll leave
this to someone who is more educated with cmake than I.

 
> I'll take a closer look when I get a chance.

Hope my preparation is some welcome kick-start.  I wonder whether some
of our patches could be forwarded upstream to reduce the number of edits
for any new version. 

Kind regards
    Andreas.