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statgen / savvy

Interface to various variant calling formats.
Mozilla Public License 2.0
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Download failed with error 404 for: //zlib.net/zlib-1.2.11.tar.gz #25

Closed psammarco closed 2 years ago

psammarco commented 2 years ago

Hello @CreRecombinase ,

I am trying to install SAIGE which pulls savvy as cget dependency. However savvy fails to build as result of a dead zlib link.

could you please fix the bit of the code that points to a dead zlib link?

Downloading http://zlib.net/zlib-1.2.11.tar.gz
  [----------------------------------------------------------------------]    0%
Download failed with error 404 for: //zlib.net/zlib-1.2.11.tar.gz
Failed to build package statgen/savvy
ERROR: configuration failed for package ‘SAIGE’
* removing ‘/usr/local/lib/R/site-library/SAIGE’
Warning message:
In i.p(...) :
  installation of package ‘/tmp/RtmpE6Jk4z/file2b3272197cc98/SAIGE_0.42.1.tar.gz’ had non-zero exit status
>

The correct link is https://zlib.net/fossils/zlib-1.2.11.tar.gz

Regards

jonathonl commented 2 years ago

Yes, this has been fixed in the master branch of Savvy, but SAIGE is not using the latest commit. You can get around this by taking the following steps.

  1. Remove line 20 (https://github.com/weizhouUMICH/SAIGE/blob/master/configure#L20) from the configure script.
  2. Runcget install -DCMAKE_C_FLAGS="-fPIC" -DCMAKE_CXX_FLAGS="-fPIC" --prefix thirdParty/cget https://zlib.net/fossils/zlib-1.2.11.tar.gz.
  3. Run the the normal install command (R CMD INSTALL --library=path_to_final_SAIGE_library SAIGE).
psammarco commented 2 years ago

Hello, apparently removing just line 20 didn't seem to be enough. I removed line 19 to line 22 and did the trick.

Thank you!