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0001-r-packages-base-Downgrade-from-3.3.2-to-3.3.1.patch
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From 9fe26dcd67b39098e65c9034f776b03d959838a3 Mon Sep 17 00:00:00 2001
From: Ray Donnelly <[email protected]>
Date: Thu, 12 Jan 2017 10:55:12 +0000
Subject: [PATCH] r-{packages,base}: Downgrade from 3.3.2 to 3.3.1
---
python/rpy2/meta.yaml | 2 +-
.../0011-Linux-Do-not-modify-LD_LIBRARY_PATH.patch | 80 +++++++++-------------
r-base/meta.yaml | 7 +-
r-packages/r-essentials/meta.yaml | 27 ++++----
r-recommended/meta.yaml | 4 +-
r/meta.yaml | 9 ++-
6 files changed, 57 insertions(+), 72 deletions(-)
diff --git a/python/rpy2/meta.yaml b/python/rpy2/meta.yaml
index 2594daf..06bd1ac 100644
--- a/python/rpy2/meta.yaml
+++ b/python/rpy2/meta.yaml
@@ -42,7 +42,7 @@ requirements:
- gcc # [not win]
- python
- setuptools
- - r
+ - r-base 3.3.1
- singledispatch # [not (py34 or py35)]
- six
- readline # [not win]
diff --git a/r-base/0011-Linux-Do-not-modify-LD_LIBRARY_PATH.patch b/r-base/0011-Linux-Do-not-modify-LD_LIBRARY_PATH.patch
index 8b7df63..9168a3c 100644
--- a/r-base/0011-Linux-Do-not-modify-LD_LIBRARY_PATH.patch
+++ b/r-base/0011-Linux-Do-not-modify-LD_LIBRARY_PATH.patch
@@ -1,6 +1,6 @@
-diff -urN R-3.3.2.orig/configure R-3.3.2/configure
---- R-3.3.2.orig/configure 2016-12-06 14:50:35.000000000 +0000
-+++ R-3.3.2/configure 2016-12-06 14:50:35.000000000 +0000
+diff -urN R-3.3.1.old/configure R-3.3.1/configure
+--- R-3.3.1.old/configure 2016-10-21 13:04:51.588700987 +0100
++++ R-3.3.1/configure 2016-10-21 13:09:48.000000000 +0100
@@ -777,6 +777,7 @@
USE_EXPORTFILES_TRUE
SHLIB_EXT
@@ -9,16 +9,16 @@ diff -urN R-3.3.2.orig/configure R-3.3.2/configure
DYLIB_UNDEFINED_ALLOWED_FALSE
DYLIB_UNDEFINED_ALLOWED_TRUE
INTERNET_LIBS
-@@ -22363,7 +22364,7 @@
-
+@@ -22355,7 +22356,7 @@
+
### * Checks for libraries.
-
+
-## Set up LD_LIBRARY_PATH or equivalent.
+## Add -Wl,-rpath, entries to RPATH_LDFLAGS.
## <FIXME>
## What is this doing *HERE*?
## Should be needed for tests using AC_RUN_IFELSE()?
-@@ -22396,6 +22397,13 @@
+@@ -22388,6 +22389,13 @@
else
R_LD_LIBRARY_PATH="${R_LD_LIBRARY_PATH}${separator}${lib}"
fi
@@ -32,10 +32,10 @@ diff -urN R-3.3.2.orig/configure R-3.3.2/configure
;;
esac
done
-@@ -22415,13 +22423,20 @@
+@@ -22407,13 +22415,20 @@
Rshlibpath_var=${shlibpath_var}
esac
-
+
-## Export LD_LIBRARY_PATH or equivalent.
+## Export LD_LIBRARY_PATH or equivalent (except we do not want to do that
+## instead we want to use -Wl,-rpath .. only doing this for Linux for now).
@@ -52,40 +52,22 @@ diff -urN R-3.3.2.orig/configure R-3.3.2/configure
+ eval "export ${Rshlibpath_var}"
+ ;;
+esac
-
-
+
+
## record how to strip shared/dynamic libraries.
-@@ -25082,7 +25097,7 @@
- # flags.
- r_save_CFLAGS=$CFLAGS
- CFLAGS="$CFLAGS $r_verb"
--(eval echo $as_me:25068: \"$ac_link\") >&5
-+(eval echo $as_me:25117: \"$ac_link\") >&5
- r_c_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'`
- echo "$r_c_v_output" >&5
- CFLAGS=$r_save_CFLAGS
-@@ -25157,7 +25172,7 @@
- # flags.
- r_save_CFLAGS=$CFLAGS
- CFLAGS="$CFLAGS $r_cv_prog_c_v"
--(eval echo $as_me:25143: \"$ac_link\") >&5
-+(eval echo $as_me:25192: \"$ac_link\") >&5
- r_c_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'`
- echo "$r_c_v_output" >&5
- CFLAGS=$r_save_CFLAGS
-diff -urN R-3.3.2.orig/configure.ac R-3.3.2/configure.ac
---- R-3.3.2.orig/configure.ac 2016-12-06 14:50:35.000000000 +0000
-+++ R-3.3.2/configure.ac 2016-12-06 14:50:35.000000000 +0000
-@@ -668,7 +668,7 @@
-
+diff -urN R-3.3.1.old/configure.ac R-3.3.1/configure.ac
+--- R-3.3.1.old/configure.ac 2016-10-21 13:04:45.171835484 +0100
++++ R-3.3.1/configure.ac 2016-10-21 13:10:13.000000000 +0100
+@@ -663,7 +663,7 @@
+
### * Checks for libraries.
-
+
-## Set up LD_LIBRARY_PATH or equivalent.
+## Add -Wl,-rpath, entries to RPATH_LDFLAGS.
## <FIXME>
## What is this doing *HERE*?
## Should be needed for tests using AC_RUN_IFELSE()?
-@@ -695,6 +695,7 @@
+@@ -690,6 +690,7 @@
-L*)
lib=`echo ${arg} | sed "s/^-L//"`
R_SH_VAR_ADD(R_LD_LIBRARY_PATH, [${lib}], [${PATH_SEPARATOR}])
@@ -93,7 +75,7 @@ diff -urN R-3.3.2.orig/configure.ac R-3.3.2/configure.ac
;;
esac
done
-@@ -714,13 +715,20 @@
+@@ -709,13 +710,20 @@
Rshlibpath_var=${shlibpath_var}
esac
AC_SUBST(shlibpath_var)
@@ -114,19 +96,19 @@ diff -urN R-3.3.2.orig/configure.ac R-3.3.2/configure.ac
+ ;;
+esac
AC_SUBST(Rshlibpath_var)
-
+
## record how to strip shared/dynamic libraries.
-@@ -1714,6 +1722,7 @@
-
+@@ -1706,6 +1714,7 @@
+
AC_SUBST(MAIN_LD)
AC_SUBST(MAIN_LDFLAGS)
+AC_SUBST(RPATH_LDFLAGS)
AC_SUBST(CPICFLAGS)
AC_SUBST(CXXPICFLAGS)
AC_SUBST(DYLIB_LD)
-diff -urN R-3.3.2.orig/etc/ldpaths.in R-3.3.2/etc/ldpaths.in
---- R-3.3.2.orig/etc/ldpaths.in 2016-12-06 14:50:35.000000000 +0000
-+++ R-3.3.2/etc/ldpaths.in 2016-12-06 14:50:35.000000000 +0000
+diff -urN R-3.3.1.old/etc/ldpaths.in R-3.3.1/etc/ldpaths.in
+--- R-3.3.1.old/etc/ldpaths.in 2016-01-09 23:15:11.000000000 +0000
++++ R-3.3.1/etc/ldpaths.in 2016-10-21 13:05:20.052916181 +0100
@@ -1,3 +1,17 @@
+# https://github.com/conda/conda/issues/1679:
+# Internally R_system() calls system() which
@@ -145,9 +127,9 @@ diff -urN R-3.3.2.orig/etc/ldpaths.in R-3.3.2/etc/ldpaths.in
: ${JAVA_HOME=@JAVA_HOME@}
: ${R_JAVA_LD_LIBRARY_PATH=@R_JAVA_LD_LIBRARY_PATH@}
if test -n "@R_LD_LIBRARY_PATH@"; then
-diff -urN R-3.3.2.orig/etc/Makeconf.in R-3.3.2/etc/Makeconf.in
---- R-3.3.2.orig/etc/Makeconf.in 2016-12-06 14:50:35.000000000 +0000
-+++ R-3.3.2/etc/Makeconf.in 2016-12-06 14:50:35.000000000 +0000
+diff -urN R-3.3.1.old/etc/Makeconf.in R-3.3.1/etc/Makeconf.in
+--- R-3.3.1.old/etc/Makeconf.in 2016-03-16 23:04:44.000000000 +0000
++++ R-3.3.1/etc/Makeconf.in 2016-10-21 13:05:20.052916181 +0100
@@ -71,7 +71,8 @@
## needed to build applications linking to static libR
MAIN_LD = @MAIN_LD@
@@ -158,9 +140,9 @@ diff -urN R-3.3.2.orig/etc/Makeconf.in R-3.3.2/etc/Makeconf.in
MKINSTALLDIRS = $(R_HOME)/bin/mkinstalldirs
OBJC = @OBJC@
OBJCFLAGS = @OBJCFLAGS@ $(LTO)
-diff -urN R-3.3.2.orig/Makeconf.in R-3.3.2/Makeconf.in
---- R-3.3.2.orig/Makeconf.in 2016-12-06 14:50:35.000000000 +0000
-+++ R-3.3.2/Makeconf.in 2016-12-06 14:50:35.000000000 +0000
+diff -urN R-3.3.1.old/Makeconf.in R-3.3.1/Makeconf.in
+--- R-3.3.1.old/Makeconf.in 2015-09-08 23:15:15.000000000 +0100
++++ R-3.3.1/Makeconf.in 2016-10-21 13:05:20.052916181 +0100
@@ -63,7 +63,8 @@
MAIN_FFLAGS = @MAIN_FFLAGS@
MAIN_LD = @MAIN_LD@@BUILD_LTO_TRUE@ $(CFLAGS)
diff --git a/r-base/meta.yaml b/r-base/meta.yaml
index 898d7eb..9875852 100644
--- a/r-base/meta.yaml
+++ b/r-base/meta.yaml
@@ -1,6 +1,6 @@
{% set native = 'm2w64-' if win else '' %}
{% set posix= 'm2-' if win else '' %}
-{% set ver= '3.3.2' %}
+{% set ver= '3.3.1' %}
package:
name: r-base
@@ -8,7 +8,8 @@ package:
source:
url: https://cran.r-project.org/src/base/R-3/R-{{ ver }}.tar.gz
- sha1: 0e39e9c2d28fe6bab9c55ca23e08ba8727fd2fca
+# sha1: 0e39e9c2d28fe6bab9c55ca23e08ba8727fd2fca
+ sha1: df853188d3e2b1c2d32393016401c432a5192c4d
patches:
- mac-unicode.patch # [osx]
- 0002-Win32-Fix-trio-config-h-include-depth-issue.patch
@@ -23,7 +24,7 @@ source:
- 0012-macOS-include-cairo_h-not-cairo-xlib_h.patch
build:
- number: 1
+ number: 6
rpaths:
- lib/R/lib/
- lib/
diff --git a/r-packages/r-essentials/meta.yaml b/r-packages/r-essentials/meta.yaml
index e4b31ae..daf87ec 100644
--- a/r-packages/r-essentials/meta.yaml
+++ b/r-packages/r-essentials/meta.yaml
@@ -1,18 +1,18 @@
package:
name: r-essentials
- version: 1.5.1
+ version: 1.4.2
requirements:
# Not really needed, but just to make sure that they are built
build:
- - r-base >=3.3.2
- - r-recommended >=3.3.2
- - r-ggplot2 >=2.2.0
+ - r-base >=3.3.1
+ - r-recommended >=3.3.1
+ - r-ggplot2 >=2.1.0
- r-plyr >=1.8.4
- r-reshape2 >=1.4.2
- r-dplyr >=0.5.0
- r-tidyr >=0.6.0
- - r-caret >=6.0_73
+ - r-caret >=6.0_70
- r-randomforest >=4.6_12
- r-data.table >=1.10.0
- r-quantmod >=0.4_7
@@ -21,8 +21,8 @@ requirements:
- r-glmnet >=2.0_5
- r-jsonlite >=1.1
- r-zoo >=1.7_13
- - r-irkernel >=0.7.1
- - r-rbokeh >=0.5.0
+ - r-irkernel >=0.6.1
+ - r-rbokeh >=0.4.2
- r-formatr >=1.4
- notebook >=4.2.3
- r-tidyverse >=1.0.0
@@ -45,16 +45,15 @@ requirements:
- r-tidyr >=0.6.0
- r-xml2 >=1.0.0
-
run:
- - r-base >=3.3.2
- - r-recommended >=3.3.2
- - r-ggplot2 >=2.2.0
+ - r-base >=3.3.1
+ - r-recommended >=3.3.1
+ - r-ggplot2 >=2.1.0
- r-plyr >=1.8.4
- r-reshape2 >=1.4.2
- r-dplyr >=0.5.0
- r-tidyr >=0.6.0
- - r-caret >=6.0_73
+ - r-caret >=6.0_70
- r-randomforest >=4.6_12
- r-data.table >=1.10.0
- r-quantmod >=0.4_7
@@ -63,8 +62,8 @@ requirements:
- r-glmnet >=2.0_5
- r-jsonlite >=1.1
- r-zoo >=1.7_13
- - r-irkernel >=0.7.1
- - r-rbokeh >=0.5.0
+ - r-irkernel >=0.6.1
+ - r-rbokeh >=0.4.2
- r-formatr >=1.4
- notebook >=4.2.3
- r-tidyverse >=1.0.0
diff --git a/r-recommended/meta.yaml b/r-recommended/meta.yaml
index 8d4fa9b..9f7df75 100644
--- a/r-recommended/meta.yaml
+++ b/r-recommended/meta.yaml
@@ -1,10 +1,10 @@
package:
name: r-recommended
- version: 3.3.2
+ version: 3.3.1
requirements:
run:
- - r-base 3.3.2
+ - r-base 3.3.1
- r-boot
- r-class
- r-cluster
diff --git a/r/meta.yaml b/r/meta.yaml
index 132eab0..fb1d23d 100644
--- a/r/meta.yaml
+++ b/r/meta.yaml
@@ -1,8 +1,11 @@
package:
name: r
- version: 3.3.2
+ version: 3.3.1
+
+build:
+ number: 1
requirements:
run:
- - r-base 3.3.2
- - r-recommended 3.3.2
+ - r-base 3.3.1 6
+ - r-recommended 3.3.1
--
2.10.1