test fix

vr1087 · vr1087 · commit b07569d9b9c6 · 2025-06-18T11:20:14.000-05:00
diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
@@ -18,8 +18,8 @@ build:
     - CFLAGS
     - CXXFLAGS
   script: |
-    export CFLAGS="-I${PREFIX}/include $CFLAGS"
-    export CXXFLAGS="-I${PREFIX}/include $CXXFLAGS"
+    export CFLAGS="-D_GNU_SOURCE -I${PREFIX}/include $CFLAGS"
+    export CXXFLAGS="-D_GNU_SOURCE -I${PREFIX}/include $CXXFLAGS"
     
     cmake -S cpp/all -B build -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_BUILD_TYPE=Release
     cmake --build build --parallel ${CPU_COUNT:-1}
diff --git a/cpp/cmake/htslib.cmake b/cpp/cmake/htslib.cmake
@@ -61,7 +61,7 @@ else()
     URL https://github.com/samtools/htslib/releases/download/1.22/htslib-1.22.tar.bz2
     BUILD_IN_SOURCE 1
     UPDATE_COMMAND ""
-    CONFIGURE_COMMAND env CFLAGS="$ENV{CFLAGS} -D_GNU_SOURCE" CXXFLAGS="$ENV{CXXFLAGS} -D_GNU_SOURCE" autoreconf -i && ./configure --prefix=${htslib_PREFIX} ${disable_flags}
+    CONFIGURE_COMMAND autoreconf -i && ./configure --prefix=${htslib_PREFIX} ${disable_flags}
     BUILD_COMMAND ${MAKE_COMMAND} lib-static
     INSTALL_COMMAND ${MAKE_COMMAND} install prefix=${htslib_INSTALL}
   )

Original file line number	Diff line number	Diff line change
`@@ -61,7 +61,7 @@ else()`
`61`	`61`	`URL https://github.com/samtools/htslib/releases/download/1.22/htslib-1.22.tar.bz2`
`62`	`62`	`BUILD_IN_SOURCE 1`
`63`	`63`	`UPDATE_COMMAND ""`
`64`		`- CONFIGURE_COMMAND env CFLAGS="$ENV{CFLAGS} -D_GNU_SOURCE" CXXFLAGS="$ENV{CXXFLAGS} -D_GNU_SOURCE" autoreconf -i && ./configure --prefix=${htslib_PREFIX} ${disable_flags}`
	`64`	`+ CONFIGURE_COMMAND autoreconf -i && ./configure --prefix=${htslib_PREFIX} ${disable_flags}`
`65`	`65`	`BUILD_COMMAND ${MAKE_COMMAND} lib-static`
`66`	`66`	`INSTALL_COMMAND ${MAKE_COMMAND} install prefix=${htslib_INSTALL}`
`67`	`67`	`)`