Update FINEMAP to 1.4.2 (#51978)

* bump/finemap

* add run_exports to FINEMAP recipe

* add script and build info

* include compiler since this package is not noarch

* only build on linux

* add outline for osx

hopefully someone more knowledgeable than me will be able to figure out how to make osx work too

The osx build is unable to find shared libraries. I tried using install_name_tool to replace the paths to the libraries, but I couldn't get it to work

* add suggestions from PR review

Thanks, Martin!

* skip building finemap if not linux64

* add license file and use noarch generic now

* completely give up on osx

The OSX binary will not work. It needs to be relinked so that the shared library paths point to the conda versions. But relinking doesn't work because the binary was not built with the -headerpad_max_install_names option

* remove noarch generic

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

* skip noarch generic lint

* add required dependencies, use LICENSE from source, and use example data for tests

* skip more lint checks

* move build requirements to host and whitelist

---------

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Co-authored-by: richard-burhans <burhans@bx.psu.edu>

recipes/finemap/meta.yaml

@@ -1,37 +1,65 @@
-# This file created by conda-build 3.22.0
-# meta.yaml template originally from:
-# /home/conda/conda-forge/recipes/finemap, last modified Thu Oct 20 22:53:08 2022
-# ------------------------------------------------
+{% set name = "finemap" %}
+{% set version = "1.4.2" %}
 
 package:
-  name: finemap
-  version: 1.4.1
+  name: {{ name }}
+  version: {{ version }}
+
 source:
-  sha256: 75c919d9cc981bc08e1a982b1632110109ffe6a057e803c9aa36c143aa56d546
-  url: http://www.christianbenner.com/finemap_v1.4.1_x86_64.tgz
+  - url: http://www.christianbenner.com/finemap_v{{ version }}_x86_64.tgz
+    sha256: 3b1fc6eb3c2ccafd647b32e02d0244495cd0ade9ed7d474606c31ebf6e98b0c9
+
 build:
-  binary_relocation: false
-  noarch: generic
-  number: '0'
+  number: 0
+  # skip osx since binary cannot be relinked b/c it was built without the -headerpad_max_install_names option
+  skip: True # [not linux64]
+  run_exports:
+    - {{ pin_subpackage('finemap', max_pin="x") }}
   script:
-    - install -Dd ${PREFIX}/bin
-    - install -D -m 755 finemap_v1.4.1_x86_64 ${PREFIX}/bin/finemap
-  string: '0'
+    - mkdir -p ${PREFIX}/bin
+    - install -m 755 finemap_v{{ version }}_x86_64 ${PREFIX}/bin/finemap
+  missing_dso_whitelist:
+    - /lib64/libdl.so.2
+    - /lib64/libm.so.6
+    - $RPATH/libgomp.so.1
+    - /lib64/libgcc_s.so.1
+    - /lib64/libpthread.so.0
+    - /lib64/libc.so.6
+    - /lib64/ld-linux-x86-64.so.2
+
 requirements:
-  build: []
-  host: []
-  run: []
+  host:
+    - {{ stdlib("c") }}
+    - libgomp
+    - libgcc
+  run:
+    - {{ stdlib("c") }}
+    - libgomp
+    - libgcc
+
 test:
+  source_files:
+    - example
   commands:
-    - test -f $PREFIX/bin/finemap
+    - finemap --help
+    - finemap --sss --in-files example/data
+    - finemap --cond --in-files example/data
+    - finemap --config --in-files example/data --rsids rs30,rs11
+
 about:
   home: http://www.christianbenner.com
-  license: Other
+  license: Custom Academic
+  license_url: http://www.christianbenner.com/license_finemap_v1.4.html
+  # use LICENSE file in downloaded source
   license_file: LICENSE
-  summary: Program for identifying causal SNPs and their effect sizes and heritability
-    contributions
+  summary: >
+    Program for identifying causal SNPs and their effect sizes and heritability contributions
+
 extra:
-  copy_test_source_files: true
-  final: true
+  skip-lints:
+    - should_use_compilers
+    - should_be_noarch_generic
+    - version_constraints_missing_whitespace
   recipe-maintainers:
+    - aryarm
     - danielnachun