CVS commit: pkgsrc/math/R

To: pkgsrc-changes%NetBSD.org@localhost
Subject: CVS commit: pkgsrc/math/R
From: "Thomas Klausner" <wiz%netbsd.org@localhost>
Date: Wed, 23 Mar 2022 21:16:44 +0000

Module Name:    pkgsrc
Committed By:   wiz
Date:           Wed Mar 23 21:16:44 UTC 2022

Modified Files:
        pkgsrc/math/R: Makefile Makefile.extension PLIST.Darwin buildlink3.mk
            distinfo
        pkgsrc/math/R/patches: patch-configure.ac

Log Message:
R: remove superfluous "-Wl," in configure patch

Bump PKGREVISION.

Fix some pkglint while here.


To generate a diff of this commit:
cvs rdiff -u -r1.231 -r1.232 pkgsrc/math/R/Makefile
cvs rdiff -u -r1.27 -r1.28 pkgsrc/math/R/Makefile.extension
cvs rdiff -u -r1.11 -r1.12 pkgsrc/math/R/PLIST.Darwin
cvs rdiff -u -r1.14 -r1.15 pkgsrc/math/R/buildlink3.mk
cvs rdiff -u -r1.94 -r1.95 pkgsrc/math/R/distinfo
cvs rdiff -u -r1.5 -r1.6 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:1.231 pkgsrc/math/R/Makefile:1.232
--- pkgsrc/math/R/Makefile:1.231        Sat Mar 19 23:13:59 2022
+++ pkgsrc/math/R/Makefile      Wed Mar 23 21:16:44 2022
@@ -1,10 +1,11 @@
-# $NetBSD: Makefile,v 1.231 2022/03/19 23:13:59 brook Exp $
+# $NetBSD: Makefile,v 1.232 2022/03/23 21:16:44 wiz Exp $
 
 #
 # If updating this package, please try to ensure PLIST.Darwin is kept in sync
 # to avoid unnecessarily breaking macOS users.
 #
 DISTNAME=      R-4.1.3
+PKGREVISION=   1
 CATEGORIES=    math
 MASTER_SITES=  ${MASTER_SITE_R_CRAN:=base/R-4/}
 
@@ -61,7 +62,7 @@ PLIST.x11=            yes
 # BLAS/LAPACK by default and only on request accelerate. Just
 # BLAS_ACCEPTED=       ${_BLAS_TYPES} accelerate.framework
 # (here and in buildlink3.mk) and deleting the first conditional
-# branch might work, given that R knows what todo with 
+# branch might work, given that R knows what todo with
 # -framework Accelerate. Someone on Darwin really needs to test.
 .if exists(/System/Library/Frameworks/Accelerate.framework)
 CONFIGURE_ARGS+=       --with-blas="-framework Accelerate"
@@ -156,7 +157,7 @@ CTF_FILES_SKIP+=    lib/R/library/mgcv/libs
 CHECK_WRKREF_SKIP+=    lib/R/etc/Makeconf
 
 pre-configure:
-       ${RUN} cd ${WRKSRC} && autoreconf -fvi || echo Ignore the warnings from autoreconf
+       ${RUN} cd ${WRKSRC} && autoreconf -fvi || ${ECHO} Ignore the warnings from autoreconf
 
 # Fix library names.  Relies on build system using -headerpad_max_install_names.
 .if ${OPSYS} == "Darwin"

Index: pkgsrc/math/R/Makefile.extension
diff -u pkgsrc/math/R/Makefile.extension:1.27 pkgsrc/math/R/Makefile.extension:1.28
--- pkgsrc/math/R/Makefile.extension:1.27       Fri Jul 31 17:04:12 2020
+++ pkgsrc/math/R/Makefile.extension    Wed Mar 23 21:16:44 2022
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile.extension,v 1.27 2020/07/31 17:04:12 brook Exp $
+# $NetBSD: Makefile.extension,v 1.28 2022/03/23 21:16:44 wiz Exp $
 #
 # This Makefile fragment is included by packages for R library packages.
 #
@@ -70,7 +70,7 @@ R_PKG_INSTALL_ARGS+=  --configure-args='$
 .endif
 
 GENERATE_PLIST+=       ( cd ${DESTDIR}${PREFIX}; for dir in ${R_INST_DIRS}; do \
-       ${FIND} ${R_LIB}/$${dir} \( -type f -o -type l \) -print; done ) | ${SORT} -u;
+                       ${FIND} ${R_LIB}/$${dir} \( -type f -o -type l \) -print; done ) | ${SORT} -u;
 
 INSTALL_TEMPLATES+=    ../../math/R/files/pkg-index.tmpl
 DEINSTALL_TEMPLATES+=  ../../math/R/files/pkg-index.tmpl

Index: pkgsrc/math/R/PLIST.Darwin
diff -u pkgsrc/math/R/PLIST.Darwin:1.11 pkgsrc/math/R/PLIST.Darwin:1.12
--- pkgsrc/math/R/PLIST.Darwin:1.11     Tue Dec  7 12:42:15 2021
+++ pkgsrc/math/R/PLIST.Darwin  Wed Mar 23 21:16:44 2022
@@ -1,17 +1,17 @@
-@comment $NetBSD: PLIST.Darwin,v 1.11 2021/12/07 12:42:15 jperkin Exp $
-@comment 
+@comment $NetBSD: PLIST.Darwin,v 1.12 2022/03/23 21:16:44 wiz Exp $
+@comment
 @comment The configure script has explicit check for darwin and sets
 @comment   --with-internal-tzcode=yes
 @comment which results in these files in lib/R/share/zoneinfo
-@comment 
+@comment
 @comment This source file:
 @comment   https://svn.r-project.org/R/trunk/src/extra/tzone/Notes
 @comment explains that osx has problems stemming from 32 bit limitations in zic.
 @comment Some further discussion found at
 @comment   https://github.com/tzinfo/tzinfo-data/issues/1
-@comment 
+@comment
 @comment Even darwin 10.10.3 (osx 14D131) still shows zic --version of 7.116
-@comment 
+@comment
 lib/R/share/zoneinfo/Africa/Abidjan
 lib/R/share/zoneinfo/Africa/Accra
 lib/R/share/zoneinfo/Africa/Addis_Ababa

Index: pkgsrc/math/R/buildlink3.mk
diff -u pkgsrc/math/R/buildlink3.mk:1.14 pkgsrc/math/R/buildlink3.mk:1.15
--- pkgsrc/math/R/buildlink3.mk:1.14    Mon Oct 12 21:51:58 2020
+++ pkgsrc/math/R/buildlink3.mk Wed Mar 23 21:16:44 2022
@@ -1,4 +1,4 @@
-# $NetBSD: buildlink3.mk,v 1.14 2020/10/12 21:51:58 bacon Exp $
+# $NetBSD: buildlink3.mk,v 1.15 2022/03/23 21:16:44 wiz Exp $
 
 BUILDLINK_TREE+=       R
 
@@ -8,7 +8,6 @@ R_BUILDLINK3_MK:=
 BUILDLINK_API_DEPENDS.R+=      R>=1.7.0
 BUILDLINK_ABI_DEPENDS.R+=      R>=4.0.3nb1
 BUILDLINK_PKGSRCDIR.R?=                ../../math/R
-.endif # R_BUILDLINK3_MK
 
 .include "../../archivers/bzip2/buildlink3.mk"
 .include "../../archivers/xz/buildlink3.mk"
@@ -17,5 +16,6 @@ BUILDLINK_PKGSRCDIR.R?=               ../../math/R
 .if !exists(/System/Library/Frameworks/Accelerate.framework)
 .include "../../mk/blas.buildlink3.mk"
 .endif
+.endif # R_BUILDLINK3_MK
 
 BUILDLINK_TREE+=       -R

Index: pkgsrc/math/R/distinfo
diff -u pkgsrc/math/R/distinfo:1.94 pkgsrc/math/R/distinfo:1.95
--- pkgsrc/math/R/distinfo:1.94 Sat Mar 19 23:13:59 2022
+++ pkgsrc/math/R/distinfo      Wed Mar 23 21:16:44 2022
@@ -1,9 +1,9 @@
-$NetBSD: distinfo,v 1.94 2022/03/19 23:13:59 brook Exp $
+$NetBSD: distinfo,v 1.95 2022/03/23 21:16:44 wiz Exp $
 
 BLAKE2s (R-4.1.3.tar.gz) = bee2174be0be0102367553b25fbf38b1ed2324a9193310a3fe98babec69b7988
 SHA512 (R-4.1.3.tar.gz) = cb71cc6c9551cc9cef4819ed778a8d0ef40490ec2bed27669c8e93d464a93bef5e73c2a03a714db03c87112b291a752ec2d21194e5abef81d85cb6c62643127c
 Size (R-4.1.3.tar.gz) = 35026517 bytes
-SHA1 (patch-configure.ac) = 967450ec49d375cce254e108b062ad73857d261d
+SHA1 (patch-configure.ac) = d6661984716a131bbfa1a2aa56385c535881d43d
 SHA1 (patch-m4_R.m4) = 704d5514e10adf0b5217bb71b06f44a612eca6e0
 SHA1 (patch-src_library_stats_src_Makefile.in) = 4eb93292858392792c37a706399e2cef91821bbe
 SHA1 (patch-src_main_character.c) = 842ae5d291f36f2beead4d32c1d41b18cbff878d

Index: pkgsrc/math/R/patches/patch-configure.ac
diff -u pkgsrc/math/R/patches/patch-configure.ac:1.5 pkgsrc/math/R/patches/patch-configure.ac:1.6
--- pkgsrc/math/R/patches/patch-configure.ac:1.5        Sat Mar 19 23:13:59 2022
+++ pkgsrc/math/R/patches/patch-configure.ac    Wed Mar 23 21:16:44 2022
@@ -1,4 +1,4 @@
-$NetBSD: patch-configure.ac,v 1.5 2022/03/19 23:13:59 brook Exp $
+$NetBSD: patch-configure.ac,v 1.6 2022/03/23 21:16:44 wiz Exp $
 
 Do not include system paths in R_LD_LIBRARY_PATH.
 NetBSD, FreeBSD, DragonFly, Darwin and Solaris fixes
@@ -18,7 +18,7 @@ NetBSD, FreeBSD, DragonFly, Darwin and S
  ## As from R 3.2.0 split up -L... and -lR
  if test "${want_R_shlib}" = yes; then
 -  LIBR0="-L\"\$(R_HOME)/lib\$(R_ARCH)\""
-+  LIBR0="-Wl,@COMPILER_RPATH_FLAG@${prefix}/lib/R/lib\$(R_ARCH) -L\"\$(R_HOME)/lib\$(R_ARCH)\""
++  LIBR0="@COMPILER_RPATH_FLAG@${prefix}/lib/R/lib\$(R_ARCH) -L\"\$(R_HOME)/lib\$(R_ARCH)\""
    LIBR1=-lR
  else
    LIBR0=

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