CVS commit: pkgsrc/math/R

["Jonathan Perkin" <jperkin%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   jperkin
Date:           Tue Apr 14 10:33:41 UTC 2026

Modified Files:
        pkgsrc/math/R: Makefile distinfo
        pkgsrc/math/R/patches: patch-configure.ac

Log Message:
R: Remove system paths from R_LD_LIBRARY_PATH.

The installed ldpaths sets LD_LIBRARY_PATH despite pkgsrc having a policy of
ensuring all library paths are correct, and this resulted in incorrect
libraries being pulled in at runtime, for example during the R-Rcpp build.

Bump PKGREVISION.


To generate a diff of this commit:
cvs rdiff -u -r1.281 -r1.282 pkgsrc/math/R/Makefile
cvs rdiff -u -r1.115 -r1.116 pkgsrc/math/R/distinfo
cvs rdiff -u -r1.15 -r1.16 pkgsrc/math/R/patches/patch-configure.ac

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/math/R/Makefile
diff -u pkgsrc/math/R/Makefile:1.281 pkgsrc/math/R/Makefile:1.282
--- pkgsrc/math/R/Makefile:1.281        Thu Mar 12 11:22:57 2026
+++ pkgsrc/math/R/Makefile      Tue Apr 14 10:33:41 2026
@@ -1,10 +1,11 @@
-# $NetBSD: Makefile,v 1.281 2026/03/12 11:22:57 mef Exp $
+# $NetBSD: Makefile,v 1.282 2026/04/14 10:33:41 jperkin Exp $
 
 #
 # If updating this package, please try to ensure PLIST.Darwin is kept in sync
 # to avoid unnecessarily breaking macOS users.
 #
 DISTNAME=      R-4.5.2
+PKGREVISION=   1
 CATEGORIES=    math
 MASTER_SITES=  ${MASTER_SITE_R_CRAN:=base/R-4/}
 

Index: pkgsrc/math/R/distinfo
diff -u pkgsrc/math/R/distinfo:1.115 pkgsrc/math/R/distinfo:1.116
--- pkgsrc/math/R/distinfo:1.115        Wed Mar 25 01:47:18 2026
+++ pkgsrc/math/R/distinfo      Tue Apr 14 10:33:41 2026
@@ -1,9 +1,9 @@
-$NetBSD: distinfo,v 1.115 2026/03/25 01:47:18 maya Exp $
+$NetBSD: distinfo,v 1.116 2026/04/14 10:33:41 jperkin Exp $
 
 BLAKE2s (R-4.5.2.tar.gz) = 89aaf25d047df226ec7340bf5550db5223163bec0b5ff1d5a3bfae691aa2106a
 SHA512 (R-4.5.2.tar.gz) = abc4ff1a1b18a1f480e7bceb3267074e30453b5a571034b4c2a1c53e1650a1bafaf86bc6ca37f117a2e4f6617039dedeedef4ba8743f38720fc70e4bed2ff0a4
 Size (R-4.5.2.tar.gz) = 40546249 bytes
-SHA1 (patch-configure.ac) = 9d5d4d33a5150493812b4eb8a4991a3f5d1161c8
+SHA1 (patch-configure.ac) = 17caa1621e93a04be23fc037805fd7240a52d17b
 SHA1 (patch-src_extra_xdr_xdr__mem.c) = 2e607b070db8b24a6ad5501e9c7c1549bf1b1d82
 SHA1 (patch-src_extra_xdr_xdr__stdio.c) = 91ea16599693e9dc14e631880fbe1c52f0f2009f
 SHA1 (patch-src_include_R__ext_Error.h) = 2d1eaebff5e57d73d301f7e818daa0b959a5c0f2

Index: pkgsrc/math/R/patches/patch-configure.ac
diff -u pkgsrc/math/R/patches/patch-configure.ac:1.15 pkgsrc/math/R/patches/patch-configure.ac:1.16
--- pkgsrc/math/R/patches/patch-configure.ac:1.15       Wed Mar 25 01:47:18 2026
+++ pkgsrc/math/R/patches/patch-configure.ac    Tue Apr 14 10:33:41 2026
@@ -1,4 +1,7 @@
-$NetBSD: patch-configure.ac,v 1.15 2026/03/25 01:47:18 maya Exp $
+$NetBSD: patch-configure.ac,v 1.16 2026/04/14 10:33:41 jperkin Exp $
+
+Do not add any system paths to R_LD_LIBRARY_PATH, it conflicts at runtime
+with what has been correctly written to the RPATH.
 
 Fix Darwin -install_name path for libR.dylib
 
@@ -41,6 +44,15 @@ release    line # 
    LIBR1=-lR
  else
    LIBR0=
+@@ -936,7 +939,7 @@ case "${host_os}" in
+     ## Not so bad in later versions of Darwin, 
+     ## where DYLD_FALLBACK_LIBRARY_PATH is used (see below).
+     ;;
+-  *)
++  noboguspaths*)
+     for arg in ${LDFLAGS}; do
+       case "${arg}" in
+         -L*)
 @@ -1864,8 +1867,8 @@ dnl     ;;
      DYLIB_EXT=".dylib"
      dylib_ldflags="${darwin_dylib_ldflags}"
@@ -52,3 +64,12 @@ release    line # 
      ## don't use version in libRblas so we can replace it with any BLAS implementation
      RBLAS_LDFLAGS="-install_name libRblas.dylib -headerpad_max_install_names"
      ;;
+@@ -2895,7 +2898,7 @@ for arg in ${LDFLAGS} ${FLIBS} ${BLAS_LI
+   case "${arg}" in
+     -L*)
+       lib=`echo ${arg} | sed "s/^-L//"`
+-      r_want_lib=true
++      r_want_lib=false
+       ## don't add anything for Darwin
+       case "${host_os}" in darwin*) r_want_lib=false ;; esac
+       ## Do not add non-existent directories.