Merge pull request #93590 from lblasc/r-packages

R: remove qtbase.patch and fix few CRAN packages

pkgs/development/r-modules/default.nix

@@ -280,6 +280,7 @@ let
     mwaved = [ pkgs.fftw.dev ];
     ncdf4 = [ pkgs.netcdf ];
     nloptr = [ pkgs.nlopt pkgs.pkgconfig ];
+    n1qn1 = [ pkgs.gfortran ];
     odbc = [ pkgs.unixODBC ];
     pander = [ pkgs.pandoc pkgs.which ];
     pbdMPI = [ pkgs.openmpi ];
@@ -415,6 +416,11 @@ let
     systemfonts = [ pkgs.pkgconfig ];
     tesseract = [ pkgs.pkgconfig ];
     Cairo = [ pkgs.pkgconfig ];
+    CLVTools = [ pkgs.gsl ];
+    JMcmprsk = [ pkgs.gsl ];
+    mashr = [ pkgs.gsl ];
+    hadron = [ pkgs.gsl ];
+    AMOUNTAIN = [ pkgs.gsl ];
     Rsymphony = [ pkgs.pkgconfig pkgs.doxygen pkgs.graphviz pkgs.subversion ];
     tcltk2 = [ pkgs.tcl pkgs.tk ];
     tikzDevice = [ pkgs.which pkgs.texlive.combined.scheme-medium ];
@@ -802,7 +808,7 @@ let
     openssl = old.openssl.overrideDerivation (attrs: {
       preConfigure = ''
         patchShebangs configure
-        '';
+      '';
       PKGCONFIG_CFLAGS = "-I${pkgs.openssl.dev}/include";
       PKGCONFIG_LIBS = "-Wl,-rpath,${pkgs.openssl.out}/lib -L${pkgs.openssl.out}/lib -lssl -lcrypto";
     });
@@ -857,6 +863,12 @@ let
         '';
     });
 
+    libgeos = old.libgeos.overrideDerivation (attrs: {
+      preConfigure = ''
+        patchShebangs configure
+        '';
+    });
+
     protolite = old.protolite.overrideDerivation (attrs: {
       preConfigure = ''
         patchShebangs configure

pkgs/development/r-modules/patches/qtbase.patch

@@ -1,13 +0,0 @@
-diff -ru -x '*~' qtbase_orig/src/Makefile qtbase/src/Makefile
---- qtbase_orig/src/Makefile	2012-03-03 03:57:47.000000000 +0900
-+++ qtbase/src/Makefile	2014-11-01 23:06:51.383876323 +0900
-@@ -10,6 +10,9 @@
- 	      -DR_INCLUDES=${R_INCLUDE_DIR} \
- 	      -DCMAKE_INSTALL_PREFIX=../src; \
- 	make install
-+# I could not control RPATH via CMake. HELP WANTED!
-+	patchelf --set-rpath ${CMAKE_LIBRARY_PATH} qtbase.so
-+	find ../inst/local/ -executable -type f -print0 | xargs -0 patchelf --set-rpath ${CMAKE_LIBRARY_PATH} 
- 
- clean:
- 	rm -rf ../kdebindings-build