[ci skip] Merge PR 35647

Merge PR bioconda#35647, commits were: 
 * Update to bedops 2.4.40 and reinstate macOS build

As described in omit-bad-mutable.patch, bedops contains code that
fails to compile with recent versions of Clang. Fortunately none
of the problematic code is actually used, so we can work around
the problem simply by removing it.

Reported upstream as bedops/bedops#267.

build-fail-blacklist

@@ -51,9 +51,6 @@ recipes/bcftools/1.3.1
 # fitBeta2.cpp:158:93: error: no matching function for call to 'arma::eGlue<arma::Glue<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::eglue_plus>::i(bool) const'
 recipes/xtail
 
-# unknown c++ error
-recipes/bedops
-
 # needs patching for compilers
 recipes/logol
 

recipes/bedops/meta.yaml

@@ -1,15 +1,17 @@
+{% set version = "2.4.40" %}
+
 package:
   name: bedops
-  version: 2.4.39
+  version: {{ version }}
 
 build:
-  number: 1
-  # Unknown build error with clang-11
-  skip: True  # [OSX]
+  number: 0
 
 source:
-  url: https://github.com/bedops/bedops/archive/v2.4.39.tar.gz
-  sha256: f8bae10c6e1ccfb873be13446c67fc3a54658515fb5071663883f788fc0e4912
+  url: https://github.com/bedops/bedops/archive/v{{ version }}.tar.gz
+  sha256: 8c01db76669dc58c595e2e1b9bdb6d462f3363fc569b15c460a63a63b8b6bf30
+  patches:
+    - omit-bad-mutable.patch
 
 requirements:
   build:

recipes/bedops/omit-bad-mutable.patch

@@ -0,0 +1,76 @@
+GCC and previous Clang successfully compile const member functions that
+modify non-mutable fields when they are members of a templated class
+that is never instantiated. Recent Clang (v11 onwards) produces errors
+in this case.
+
+The problematic functions are never used, so we work around this by
+omitting them.
+
+diff --git a/applications/bed/bedextract/src/ExtractRows.cpp b/applications/bed/bedextract/src/ExtractRows.cpp
+index c5f81b6a..c15644ca 100644
+--- a/applications/bed/bedextract/src/ExtractRows.cpp
++++ b/applications/bed/bedextract/src/ExtractRows.cpp
+@@ -77,7 +77,6 @@ namespace {
+     }
+
+     bool Empty() const { return empty_; }
+-    void Clear() const { empty_ = true; }
+
+   private:
+     bool empty_;
+diff --git a/interfaces/general-headers/utility/BitMonitor.hpp b/interfaces/general-headers/utility/BitMonitor.hpp
+index f9fefdda..0eb91810 100644
+--- a/interfaces/general-headers/utility/BitMonitor.hpp
++++ b/interfaces/general-headers/utility/BitMonitor.hpp
+@@ -78,6 +78,7 @@ namespace Ext {
+       _open = 0;
+     }
+
++#if 0
+     inline std::size_t next_set(std::size_t start) const {
+       start += 1;
+       std::size_t bin = start/BASE;
+@@ -110,6 +111,7 @@ namespace Ext {
+         _open = 0;
+       return next_set(0);
+     }
++#endif
+
+     inline std::size_t next_unset(std::size_t start) {
+       start += 1;
+diff --git a/interfaces/general-headers/utility/CharPooledMemory.hpp b/interfaces/general-headers/utility/CharPooledMemory.hpp
+index 267bb604..7d6793a2 100644
+--- a/interfaces/general-headers/utility/CharPooledMemory.hpp
++++ b/interfaces/general-headers/utility/CharPooledMemory.hpp
+@@ -203,6 +203,7 @@ namespace Ext {
+         }
+
+     private:
++#if 0
+       char*
+       find_open(char const* c)
+         {
+@@ -254,6 +255,7 @@ namespace Ext {
+           } // while
+           return nullptr;
+         }
++#endif
+
+       friend struct PooledCharMemory2<nelements>;
+
+@@ -466,6 +468,7 @@ namespace Ext {
+           return clean(c, sz);
+         }
+
++#if 0
+       char*
+       clean(char const* c, std::size_t need)
+         {
+@@ -492,6 +495,7 @@ namespace Ext {
+           _dirty.clear();
+           return nullptr;
+         }
++#endif
+
+       friend struct PooledCharMemory<nelements>;
+